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ClawBio/ClawBio
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
History
Review weekly changes to SKILL.md before updating. Dates mark the weeks in which we observed each version; checks apply to the recorded commits.
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skills/affinity-proteomics/SKILL.md
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skills/analyze-fasta/SKILL.md
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skills/ancestry-risk-profiler/SKILL.md
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skills/archaic-introgression/SKILL.md
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skills/arrayexpress-fetch/SKILL.md
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skills/article-data-fetcher/SKILL.md
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skills/bgpt-mcp/SKILL.md
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skills/bigquery-public/SKILL.md
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skills/bio-orchestrator/SKILL.md
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skills/bioconductor-bridge/SKILL.md
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skills/bioqc-mcp/SKILL.md
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skills/biostudies-fetch/SKILL.md
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skills/busco-assessor/SKILL.md
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skills/cell-detection/SKILL.md
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skills/celltype-specificity-profiler/SKILL.md
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skills/claw-amplicon-qc/SKILL.md
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skills/claw-ancestry-pca/SKILL.md
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skills/claw-metagenomics/SKILL.md
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skills/claw-methylation-cycle/SKILL.md
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skills/claw-semantic-sim/SKILL.md
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skills/clawpathy-autoresearch/SKILL.md
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skills/clawpathy-autoresearch/examples/demo_task/skill/SKILL.md
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skills/clinical-trial-finder/SKILL.md
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skills/clinical-variant-prioritizer/SKILL.md
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skills/clinical-variant-reporter/SKILL.md
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skills/clinpgx/SKILL.md
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skills/cnv-acmg-classifier/SKILL.md
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skills/crispr-screen-triage/SKILL.md
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skills/data-extractor/SKILL.md
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skills/de-summary/SKILL.md
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skills/deepspot-m/SKILL.md
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skills/diff-visualizer/SKILL.md
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skills/dnasp/SKILL.md
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skills/drug-photo/SKILL.md
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skills/drug-repurposing-screen/SKILL.md
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skills/ena-fetch/SKILL.md
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skills/eqtl-catalogue-region-fetch/SKILL.md
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skills/equity-scorer/SKILL.md
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skills/fastreer/SKILL.md
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skills/fine-mapping/SKILL.md
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skills/flow-bio/SKILL.md
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skills/galaxy-bridge/SKILL.md
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skills/genome-compare/SKILL.md
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skills/genome-match/SKILL.md
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skills/geo-fetch/SKILL.md
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skills/gi-annotation/SKILL.md
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skills/gi-chromatin/SKILL.md
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skills/gi-enhancer/SKILL.md
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skills/gi-expression/SKILL.md
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skills/gi-promoter/SKILL.md
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skills/gi-splice/SKILL.md
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skills/gwas-catalog-region-fetch/SKILL.md
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skills/gwas-lookup/SKILL.md
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skills/gwas-pipeline/SKILL.md
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skills/gwas-prs/SKILL.md
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skills/gwas-sumstats-harmonize/SKILL.md
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skills/hla-typing/SKILL.md
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skills/igv-validator/SKILL.md
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skills/illumina-bridge/SKILL.md
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skills/just-prs-mcp/SKILL.md
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skills/labstep/SKILL.md
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skills/ld-1000g-region-compute/SKILL.md
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skills/lit-synthesizer/SKILL.md
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skills/locuscompare-region-render/SKILL.md
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skills/marker-dominance-mapper/SKILL.md
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skills/mendelian-randomisation/SKILL.md
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skills/methylation-clock/SKILL.md
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skills/multiqc-reporter/SKILL.md
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skills/ncbi-datasets/SKILL.md
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skills/nfcore-rnaseq-wrapper/SKILL.md
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skills/nfcore-rnastructurome-wrapper/SKILL.md
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skills/nfcore-sarek-wrapper/SKILL.md
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skills/nfcore-scrnaseq-wrapper/SKILL.md
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skills/nutrigx/SKILL.md
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skills/omics-target-evidence-mapper/SKILL.md
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skills/organ-aging-studio/SKILL.md
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skills/pathway-enricher/SKILL.md
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skills/pharmgx-reporter/SKILL.md
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skills/phylogenetics-builder/SKILL.md
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skills/polars-bio/SKILL.md
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skills/pride-fetch/SKILL.md
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skills/profile-report/SKILL.md
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skills/proteomics-clock/SKILL.md
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skills/proteomics-de/SKILL.md
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skills/protocols-io/SKILL.md
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skills/prs-abstain/SKILL.md
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skills/prs-applicability-gate/SKILL.md
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skills/pubmed-summariser/SKILL.md
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skills/rare-disease-rnaseq/SKILL.md
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skills/rare-high-impact-variants/SKILL.md
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skills/recombinator/SKILL.md
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skills/repro-enforcer/SKILL.md
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skills/rnaseq-de/SKILL.md
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skills/sample-qc-triage/SKILL.md
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skills/scrna-embedding/SKILL.md
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skills/scrna-orchestrator/SKILL.md
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skills/seq-wrangler/SKILL.md
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skills/skill-builder/SKILL.md
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skills/spatial-transcriptomics/SKILL.md
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skills/struct-predictor/SKILL.md
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View on GitHubAdd to my skills
Verified commit df1d8ffe9facdba2b89f608569fea9daaa1fc92f
git clone --filter=blob:none --no-checkout https://github.com/ClawBio/ClawBio.git .hotskills/clawbio-clawbio && git -C .hotskills/clawbio-clawbio checkout --detach df1d8ffe9facdba2b89f608569fea9daaa1fc92f
# Copy each selected skill directory from .hotskills/clawbio-clawbio into .claude/skills/<skill-name>/git clone --filter=blob:none --no-checkout https://github.com/ClawBio/ClawBio.git .hotskills/clawbio-clawbio && git -C .hotskills/clawbio-clawbio checkout --detach df1d8ffe9facdba2b89f608569fea9daaa1fc92f
# Copy each selected skill directory from .hotskills/clawbio-clawbio into .agents/skills/<skill-name>/1.2kGitHub stars
5stars in 7 days
110skills in this repository
357commits in 30 days
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- Star growth, last 24 hoursAhead of 71% of tracked repositories
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- Commits, last 30 daysAhead of 98% of tracked repositories
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Individual skills in this repository
- affinity-proteomics
skills/affinity-proteomics - analyze-fasta
skills/analyze-fasta - ancestry-risk-profiler
skills/ancestry-risk-profiler - archaic-introgression
skills/archaic-introgression - arrayexpress-fetch
skills/arrayexpress-fetch - article-data-fetcher
skills/article-data-fetcher - bgpt-mcp
skills/bgpt-mcp - bigquery-public
skills/bigquery-public - bio-orchestrator
skills/bio-orchestrator - bioconductor-bridge
skills/bioconductor-bridge - bioqc-mcp
skills/bioqc-mcp - biostudies-fetch
skills/biostudies-fetch - busco-assessor
skills/busco-assessor - cell-detection
skills/cell-detection - celltype-specificity-profiler
skills/celltype-specificity-profiler - claw-amplicon-qc
skills/claw-amplicon-qc - claw-ancestry-pca
skills/claw-ancestry-pca - claw-metagenomics
skills/claw-metagenomics - claw-methylation-cycle
skills/claw-methylation-cycle - claw-semantic-sim
skills/claw-semantic-sim - clawpathy-autoresearch
skills/clawpathy-autoresearch - skill
skills/clawpathy-autoresearch/examples/demo_task/skill - clinical-trial-finder
skills/clinical-trial-finder - clinical-variant-prioritizer
skills/clinical-variant-prioritizer - clinical-variant-reporter
skills/clinical-variant-reporter - clinpgx
skills/clinpgx - cnv-acmg-classifier
skills/cnv-acmg-classifier - crispr-screen-triage
skills/crispr-screen-triage - data-extractor
skills/data-extractor - de-summary
skills/de-summary - deepspot-m
skills/deepspot-m - diff-visualizer
skills/diff-visualizer - dnasp
skills/dnasp - drug-photo
skills/drug-photo - drug-repurposing-screen
skills/drug-repurposing-screen - ena-fetch
skills/ena-fetch - eqtl-catalogue-region-fetch
skills/eqtl-catalogue-region-fetch - equity-scorer
skills/equity-scorer - fastreer
skills/fastreer - fine-mapping
skills/fine-mapping - flow-bio
skills/flow-bio - galaxy-bridge
skills/galaxy-bridge - genome-compare
skills/genome-compare - genome-match
skills/genome-match - geo-fetch
skills/geo-fetch - gi-annotation
skills/gi-annotation - gi-chromatin
skills/gi-chromatin - gi-enhancer
skills/gi-enhancer - gi-expression
skills/gi-expression - gi-promoter
skills/gi-promoter - gi-splice
skills/gi-splice - gwas-catalog-region-fetch
skills/gwas-catalog-region-fetch - gwas-lookup
skills/gwas-lookup - gwas-pipeline
skills/gwas-pipeline - gwas-prs
skills/gwas-prs - gwas-sumstats-harmonize
skills/gwas-sumstats-harmonize - hla-typing
skills/hla-typing - igv-validator
skills/igv-validator - illumina-bridge
skills/illumina-bridge - just-prs-mcp
skills/just-prs-mcp - labstep
skills/labstep - ld-1000g-region-compute
skills/ld-1000g-region-compute - lit-synthesizer
skills/lit-synthesizer - locuscompare-region-render
skills/locuscompare-region-render - marker-dominance-mapper
skills/marker-dominance-mapper - mendelian-randomisation
skills/mendelian-randomisation - methylation-clock
skills/methylation-clock - multiqc-reporter
skills/multiqc-reporter - ncbi-datasets
skills/ncbi-datasets - nfcore-rnaseq-wrapper
skills/nfcore-rnaseq-wrapper - nfcore-rnastructurome-wrapper
skills/nfcore-rnastructurome-wrapper - nfcore-sarek-wrapper
skills/nfcore-sarek-wrapper - nfcore-scrnaseq-wrapper
skills/nfcore-scrnaseq-wrapper - nutrigx
skills/nutrigx - omics-target-evidence-mapper
skills/omics-target-evidence-mapper - organ-aging-studio
skills/organ-aging-studio - pathway-enricher
skills/pathway-enricher - pharmgx-reporter
skills/pharmgx-reporter - phylogenetics-builder
skills/phylogenetics-builder - polars-bio
skills/polars-bio - pride-fetch
skills/pride-fetch - profile-report
skills/profile-report - proteomics-clock
skills/proteomics-clock - proteomics-de
skills/proteomics-de - protocols-io
skills/protocols-io - prs-abstain
skills/prs-abstain - prs-applicability-gate
skills/prs-applicability-gate - pubmed-summariser
skills/pubmed-summariser - rare-disease-rnaseq
skills/rare-disease-rnaseq - rare-high-impact-variants
skills/rare-high-impact-variants - recombinator
skills/recombinator - repro-enforcer
skills/repro-enforcer - rnaseq-de
skills/rnaseq-de - sample-qc-triage
skills/sample-qc-triage - scrna-embedding
skills/scrna-embedding - scrna-orchestrator
skills/scrna-orchestrator - seq-wrangler
skills/seq-wrangler - skill-builder
skills/skill-builder - spatial-transcriptomics
skills/spatial-transcriptomics - struct-predictor
skills/struct-predictor - target-validation-scorer
skills/target-validation-scorer - turingdb-graph
skills/turingdb-graph - ukb-navigator
skills/ukb-navigator - ukb-ppp-region-fetch
skills/ukb-ppp-region-fetch - variant-annotation
skills/variant-annotation - vcf-annotator
skills/vcf-annotator - wes-clinical-report-en
skills/wes-clinical-report-en - wes-clinical-report-es
skills/wes-clinical-report-es - wgs-prs
skills/wgs-prs - xena-tcga-gene-query
skills/xena-tcga-gene-query
How it works
affinity-proteomics
When your agent uses it
Unified analysis pipeline for affinity-based proteomics platforms — Olink (PEA, NPX) and SomaLogic SomaScan (SOMAmer, RFU). Platform-aware QC, normalisation, differential abundance, volcano plots, heatmaps, and PCA.
What it loads into context
Frontmatter
299 tokensAlways available to the agent
SKILL.md
1,939 tokensWhen the skill is activated
Reference documents
565,960 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- CLI Reference
- Demo
- Output Structure
- Suggested Actions
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
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No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubanalyze-fasta
When your agent uses it
Analyze a single FASTA file (nucleotide or protein), compute sequence-level metrics (GC, ORFs, MW, pI, GRAVY, secondary-structure fractions) with Biopython, and write a Markdown report plus structured JSON for downstream chaining.
What it loads into context
Frontmatter
608 tokensAlways available to the agent
SKILL.md
3,490 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyanalyze_fasta.pytests/test_analyze_fasta.py
Files
../../clawbio.pyruns735 bytesINTENTS.jsonasset692 bytesSKILL.mdcore13,654 bytesSKILL.mdcore13,654 bytesSKILL.mdcore13,654 bytesSKILL.mdcore13,654 bytesSKILL.mdcore13,654 bytesanalyze_fasta.pyruns46,857 bytesexample_data/demo_nucleotide.fastaasset801 bytesexample_data/demo_protein.fastaasset225 bytestests/test_analyze_fasta.pyruns12,559 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubancestry-risk-profiler
When your agent uses it
Infers genetic super-population ancestry from a 23andMe/AncestryDNA file and computes ancestry-stratified odds ratios with an exploratory Ancestry Elevation Score (AES) showing where ancestry-specific GWAS effect sizes diverge from European reference estimates. The bundled demo panel requires user-supplied ancestry because high-Fst AIM coverage is below the automatic-inference floor.
What it loads into context
Frontmatter
749 tokensAlways available to the agent
SKILL.md
5,860 tokensWhen the skill is activated
Reference documents
5,991 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Example Output
- Output Structure
- Scoring Methodology
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
ancestry_risk_profiler.pytests/test_ancestry_reproducibility.pytests/test_ancestry_risk_profiler.py
Files
SKILL.mdcore23,383 bytesSKILL.mdcore23,383 bytesSKILL.mdcore23,383 bytesSKILL.mdcore23,383 bytesSKILL.mdcore23,383 bytesSKILL.mdcore23,383 bytesSKILL.mdcore23,383 bytesSKILL.mdcore23,383 bytesancestry_risk_profiler.pyruns38,042 bytesdata/PROVENANCE.mddoc19,011 bytesdata/aisnp_panel.csvasset4,322 bytesdata/ancestry_risk_associations.jsonasset21,398 bytesdata/demo_patient_south_asian.txtdoc2,107 bytestests/test_ancestry_reproducibility.pyruns6,429 bytestests/test_ancestry_risk_profiler.pyruns51,357 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubarchaic-introgression
When your agent uses it
Detect Neanderthal and Denisovan introgression segments from modern human genomes
What it loads into context
Frontmatter
248 tokensAlways available to the agent
SKILL.md
2,008 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Example Queries
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Citations
Scripts executed separately
archaic_introgression.pypipeline.pytests/__init__.pytests/test_archaic_introgression.pytests/test_pipeline.py
Files
SKILL.mdcore7,808 bytesSKILL.mdcore7,808 bytesSKILL.mdcore7,808 bytesSKILL.mdcore7,808 bytesSKILL.mdcore7,808 bytesSKILL.mdcore7,808 bytesarchaic_introgression.pyruns21,587 bytesexamples/demo_archaic.vcfasset676 bytesexamples/demo_modern.vcfasset772 bytespipeline.pyruns23,552 bytestests/__init__.pyruns0 bytestests/test_archaic_introgression.pyruns12,174 bytestests/test_pipeline.pyruns10,505 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubarrayexpress-fetch
When your agent uses it
Query metadata and download data from ArrayExpress, EMBL-EBI's functional genomics collection, now hosted inside BioStudies. Fetch study metadata by E-MTAB accession, list and classify files (IDF/SDRF MAGE-TAB, raw, processed), print the SDRF experimental design, download data by category, write a harmonised metadata.tsv, and build an nf-core/rnaseq or nf-core/scrnaseq samplesheet.csv from the SDRF.
What it loads into context
Frontmatter
706 tokensAlways available to the agent
SKILL.md
6,149 tokensWhen the skill is activated
Reference documents
5,233 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyarrayexpress_fetch.pyarrayexpress_fetch_api.pytests/test_arrayexpress_fetch.py
Files
../../clawbio.pyruns735 bytes../../docs/data-handling.mddoc19,645 bytesSKILL.mdcore22,994 bytesSKILL.mdcore22,994 bytesSKILL.mdcore22,994 bytesSKILL.mdcore22,994 bytesSKILL.mdcore22,994 bytesSKILL.mdcore22,994 bytesSKILL.mdcore22,994 bytesarrayexpress_fetch.pyruns10,640 bytesarrayexpress_fetch_api.pyruns35,367 bytesexamples/demo_E-MTAB-10030.jsonasset31,682 bytesexamples/demo_E-MTAB-10030.sdrf.txtdoc7,242 bytesexamples/demo_search.jsonasset3,621 bytestests/test_arrayexpress_fetch.pyruns25,163 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubarticle-data-fetcher
When your agent uses it
Given an article DOI or PubMed ID, discover and download the genomics data files deposited by the authors (VCF, FASTA, H5AD, CSV, JSON, BAM, etc.) from public repositories such as GEO, ENA, Zenodo, Figshare, Dryad, and OSF.
What it loads into context
Frontmatter
768 tokensAlways available to the agent
SKILL.md
4,196 tokensWhen the skill is activated
Reference documents
1,171 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- Supported Repositories
- Supported File Types
- CLI Reference
- Demo
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyarticle_data_fetcher.pytests/test_article_data_fetcher.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore15,759 bytesSKILL.mdcore15,759 bytesSKILL.mdcore15,759 bytesSKILL.mdcore15,759 bytesSKILL.mdcore15,759 bytesSKILL.mdcore15,759 bytesSKILL.mdcore15,759 bytesWORKFLOW.mddoc3,799 bytesarticle_data_fetcher.pyruns42,428 bytestests/test_article_data_fetcher.pyruns3,279 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbgpt-mcp
When your agent uses it
Search scientific papers via the BGPT MCP server and retrieve structured experimental data — methods, results, conclusions, quality scores, and 25+ metadata fields per paper.
What it loads into context
Frontmatter
421 tokensAlways available to the agent
SKILL.md
3,149 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- MCP Connection Reference
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Pricing
- Citations
Scripts executed separately
../../clawbio.pytests/test_bgpt_mcp.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore12,691 bytesSKILL.mdcore12,691 bytesSKILL.mdcore12,691 bytesSKILL.mdcore12,691 bytestests/test_bgpt_mcp.pyruns5,300 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbigquery-public
When your agent uses it
Run read-only SQL against BigQuery public datasets with local result capture, cost safeguards, and reproducibility outputs.
What it loads into context
Frontmatter
210 tokensAlways available to the agent
SKILL.md
1,567 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pybigquery_backends.pybigquery_models.pybigquery_public.pybigquery_support.pytests/test_bigquery_public.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore6,300 bytesSKILL.mdcore6,300 bytesSKILL.mdcore6,300 bytesSKILL.mdcore6,300 bytesSKILL.mdcore6,300 bytesbigquery_backends.pyruns22,375 bytesbigquery_models.pyruns1,717 bytesbigquery_public.pyruns7,282 bytesbigquery_support.pyruns22,418 bytesdemo/demo_query.sqlasset119 bytesdemo/demo_result.jsonasset610 bytestests/test_bigquery_public.pyruns23,197 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbio-orchestrator
When your agent uses it
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
What it loads into context
Frontmatter
138 tokensAlways available to the agent
SKILL.md
2,612 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Routing Table
- Decision Process
- File Type Detection
- Report Template
- Multi-Skill Chaining Example
- Safety Rules
- Example Queries
Scripts executed separately
orchestrator.pytests/test_orchestrator.pytests/test_skill_intents.py
Files
SKILL.mdcore10,059 bytesSKILL.mdcore10,059 bytesSKILL.mdcore10,059 bytesorchestrator.pyruns33,830 bytestests/test_orchestrator.pyruns17,036 bytestests/test_skill_intents.pyruns35,654 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbioconductor-bridge
When your agent uses it
Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.
What it loads into context
Frontmatter
244 tokensAlways available to the agent
SKILL.md
2,366 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pybioc_recommender.pybioconductor_bridge.pytests/test_bioc_recommender.pytests/test_bioconductor_bridge.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore10,163 bytesSKILL.mdcore10,163 bytesSKILL.mdcore10,163 bytesSKILL.mdcore10,163 bytesbioc_recommender.pyruns47,778 bytesbioconductor_bridge.pyruns38,836 bytestests/test_bioc_recommender.pyruns14,493 bytestests/test_bioconductor_bridge.pyruns16,621 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbioqc-mcp
When your agent uses it
Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation. Exposes an MCP stdio server for live AI integration alongside a ClawBio CLI runner.
What it loads into context
Frontmatter
386 tokensAlways available to the agent
SKILL.md
2,178 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Example Output
- Algorithm / Methodology
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pybioqc_mcp.pytests/test_bioqc_mcp.py
Files
../../clawbio.pyruns735 bytesINTENTS.jsonasset642 bytesSKILL.mdcore8,973 bytesSKILL.mdcore8,973 bytesSKILL.mdcore8,973 bytesSKILL.mdcore8,973 bytesbioqc_mcp.pyruns49,826 bytestests/test_bioqc_mcp.pyruns3,729 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbiostudies-fetch
When your agent uses it
Query metadata and download data from EMBL-EBI BioStudies, the database that describes biological studies and links their data across collections (ArrayExpress, BioImages, BioModels, EGA-linked studies and standalone submissions). Fetch study metadata by accession, list and download attached files, search across collections, and write a harmonised metadata.tsv.
What it loads into context
Frontmatter
594 tokensAlways available to the agent
SKILL.md
4,400 tokensWhen the skill is activated
Reference documents
5,233 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pybiostudies_fetch.pybiostudies_fetch_api.pytests/test_biostudies_fetch.py
Files
../../clawbio.pyruns735 bytes../../docs/data-handling.mddoc19,645 bytesSKILL.mdcore17,017 bytesSKILL.mdcore17,017 bytesSKILL.mdcore17,017 bytesSKILL.mdcore17,017 bytesSKILL.mdcore17,017 bytesSKILL.mdcore17,017 bytesbiostudies_fetch.pyruns5,952 bytesbiostudies_fetch_api.pyruns16,504 bytesexamples/demo_S-BSST2074.jsonasset4,195 bytesexamples/demo_search.jsonasset1,497 bytestests/test_biostudies_fetch.pyruns15,500 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubbusco-assessor
When your agent uses it
Genome, transcriptome, and protein completeness assessment via BUSCO v6. Agentic lineage routing from organism description, all three BUSCO modes, auto-lineage support, and full demo mode without the BUSCO binary.
What it loads into context
Frontmatter
735 tokensAlways available to the agent
SKILL.md
5,494 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- NCBI Taxonomy Integration
- Agentic Lineage Routing
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
busco_assessor.pytests/__init__.pytests/test_busco_assessor.py
Files
SKILL.mdcore19,794 bytesSKILL.mdcore19,794 bytesSKILL.mdcore19,794 bytesSKILL.mdcore19,794 bytesSKILL.mdcore19,794 bytesSKILL.mdcore19,794 bytesSKILL.mdcore19,794 bytesSKILL.mdcore19,794 bytesbusco_assessor.pyruns40,156 bytestests/__init__.pyruns0 bytestests/test_busco_assessor.pyruns28,347 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubcell-detection
When your agent uses it
Cell segmentation in fluorescence microscopy images. Supports Cellpose/cpsam (Cellpose 4.0) with additional backends planned. Produces segmentation masks, per-cell morphology metrics (area, diameter, centroid, eccentricity), overlay figures, and a report.md.
What it loads into context
Frontmatter
317 tokensAlways available to the agent
SKILL.md
2,391 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Notes
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
cell_detection.pytests/test_cell_detection.py
Files
SKILL.mdcore8,455 bytesSKILL.mdcore8,455 bytesSKILL.mdcore8,455 bytesSKILL.mdcore8,455 bytesSKILL.mdcore8,455 bytescell_detection.pyruns27,712 bytesrequirements.txtdoc106 bytestests/test_cell_detection.pyruns38,788 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubcelltype-specificity-profiler
When your agent uses it
Given a gene and a single-cell atlas, compute how cell-type-specific its expression is — the tau specificity index, Sarle's expression bimodality coefficient, and the cell types that drive the signal; a pure analytic transform that chains downstream of scrna-embedding.
What it loads into context
Frontmatter
637 tokensAlways available to the agent
SKILL.md
4,509 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyprofiler.pytests/test_profiler.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore17,336 bytesSKILL.mdcore17,336 bytesSKILL.mdcore17,336 bytesSKILL.mdcore17,336 bytesSKILL.mdcore17,336 bytesexamples/expected_demo_profile.jsonasset2,335 bytesprofiler.pyruns13,861 bytestests/test_profiler.pyruns5,732 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclaw-amplicon-qc
When your agent uses it
16S/18S rRNA amplicon preprocessing — from raw paired-end FASTQ files through N removal and primer trimming, producing outputs ready for DADA2 quality filtering and denoising. Deliberately stops before quality-filtering decisions that require researcher judgment.
What it loads into context
Frontmatter
1,181 tokensAlways available to the agent
SKILL.md
6,523 tokensWhen the skill is activated
Reference documents
225 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
- License
Scripts executed separately
amplicon_qc.Rtests/preflight_diagnostic.Rtests/run_test.sh
Files
SKILL.mdcore25,634 bytesSKILL.mdcore25,634 bytesSKILL.mdcore25,634 bytesSKILL.mdcore25,634 bytesSKILL.mdcore25,634 bytesSKILL.mdcore25,634 bytesamplicon_qc.Rruns62,830 bytesenvironment.ymlasset989 bytestests/fixtures/README.mddoc714 bytestests/fixtures/demo_R1.fastq.gzasset47,218 bytestests/fixtures/demo_R2.fastq.gzasset66,425 bytestests/preflight_diagnostic.Rruns5,374 bytestests/run_test.shruns6,859 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclaw-ancestry-pca
When your agent uses it
Ancestry decomposition PCA against the Simons Genome Diversity Project
What it loads into context
Frontmatter
335 tokensAlways available to the agent
SKILL.md
1,381 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- What it does
- Why this exists
- Reference Panel
- Usage
- Example Output
- Output Structure
- Interpretation Guide
- Citation
Scripts executed separately
ancestry_pca.pytests/__init__.pytests/test_ancestry_pca.py
Files
SKILL.mdcore5,481 bytesSKILL.mdcore5,481 bytesSKILL.mdcore5,481 bytesSKILL.mdcore5,481 bytesSKILL.mdcore5,481 bytesancestry_pca.pyruns19,643 bytestests/__init__.pyruns0 bytestests/test_ancestry_pca.pyruns13,244 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclaw-metagenomics
When your agent uses it
Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways
What it loads into context
Frontmatter
540 tokensAlways available to the agent
SKILL.md
2,641 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- What it does
- Why this exists
- Validated On
- WHO-Critical ARG Detection
- Usage
- Example Output
- Pipeline Architecture
- Database Requirements
- Citations
Scripts executed separately
metagenomics_profiler.py
Files
SKILL.mdcore9,655 bytesSKILL.mdcore9,655 bytesSKILL.mdcore9,655 bytesSKILL.mdcore9,655 bytesmetagenomics_profiler.pyruns48,433 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclaw-methylation-cycle
When your agent uses it
Methylation cycle analysis — enzymatic activity profiles, Net Methylation Capacity, BH4 axis estimates, compound heterozygosity detection from SNP genotype data.
What it loads into context
Frontmatter
346 tokensAlways available to the agent
SKILL.md
4,722 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Workflow
- Example Output
- Gotchas
- Domain Decisions
- Safety Rules
- Agent Boundary
- Usage
- Output Structure
- References
- Changelog
Scripts executed separately
methylation_cycle.pytests/test_methylation_cycle.pytests/test_reproducibility_bundle.py
Files
SKILL.mdcore17,951 bytesSKILL.mdcore17,951 bytesSKILL.mdcore17,951 bytesSKILL.mdcore17,951 bytesSKILL.mdcore17,951 bytesSKILL.mdcore17,951 bytesSKILL.mdcore17,951 bytesdemo_input.txtdoc599 bytesmethylation_cycle.pyruns32,192 bytestests/test_methylation_cycle.pyruns13,593 bytestests/test_reproducibility_bundle.pyruns1,174 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclaw-semantic-sim
When your agent uses it
Semantic Similarity Index for disease research literature using PubMedBERT embeddings
What it loads into context
Frontmatter
245 tokensAlways available to the agent
SKILL.md
1,389 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- What it does
- Why this exists
- Key Finding
- Pipeline
- Status
- Example Output
- Interpretation Guide
- Citation
Files
SKILL.mdcore5,643 bytesSKILL.mdcore5,643 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclawpathy-autoresearch
When your agent uses it
Eval-driven skill tuning. Given a task and an LLM-judge rubric, iteratively rewrites a SKILL.md until a downstream executor agent performs well against the judge. Low-code: all evaluation is LLM-as-judge, not deterministic Python.
What it loads into context
Frontmatter
303 tokensAlways available to the agent
SKILL.md
1,351 tokensWhen the skill is activated
Reference documents
28,207 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core idea
- You are the orchestrator
- Workspace layout
- Key principles
- Safety
- Gotchas
Scripts executed separately
__init__.py__main__.pydispatcher.pyexecutor.pyjudge.pyloop.pyloop_parallel.pymultitask_loop.pyproposer.pyworkspace.py
Files
.gitignoreasset957 bytesSKILL.mdcore5,516 bytesSKILL.mdcore5,516 bytesSKILL.mdcore5,516 bytes__init__.pyruns383 bytes__main__.pyruns1,427 bytesdispatcher.pyruns2,129 bytesexamples/champions/README.mddoc1,397 bytesexamples/champions/trubetskoy_scz_finemap_0.235.mddoc50,954 bytesexamples/champions/yengo_height_ldsc_h2.mddoc26,312 bytesexamples/demo_task/README.mddoc690 bytesexamples/demo_task/rubric.mddoc1,763 bytesexamples/demo_task/task.jsonasset463 bytesexamples/presentation_intro.mddoc3,637 bytesexamples/skill_transfer_summary.pngasset120,434 bytesexecutor.pyruns1,116 bytesjudge.pyruns2,677 bytesloop.pyruns5,231 bytesloop_parallel.pyruns9,466 bytesmultitask_loop.pyruns15,503 bytesprompts/builder.mddoc2,040 bytesprompts/executor.mddoc927 bytesprompts/judge.mddoc3,702 bytesprompts/proposer.mddoc1,213 bytesprompts/scout.mddoc797 bytesproposer.pyruns1,500 bytesworkspace.pyruns3,590 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubWhen your agent uses it
What it loads into context
Frontmatter
0 tokensAlways available to the agent
SKILL.md
77 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Workflow
Files
SKILL.mdcore331 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclinical-trial-finder
When your agent uses it
Find clinical trials for a gene, variant, or condition from ClinicalTrials.gov + EUCTR, with FHIR R4 output
What it loads into context
Frontmatter
916 tokensAlways available to the agent
SKILL.md
3,014 tokensWhen the skill is activated
Reference documents
4,799 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Domain Decisions
- Output Structure
- Safety Rules
- Agent Boundary
Scripts executed separately
api.pyclinical_trial_finder.pyconstants.pydemo.sheuctr.pyexamples/demo_output/commands.shgwas_bridge.pyopentargets.pytests/test_clinical_trial_finder.pytests/test_fhir_e2e.pytests/test_gwas_bridge_v2.pywriters.py
Files
.gitignoreasset61 bytesSKILL.mdcore12,657 bytesSKILL.mdcore12,657 bytesSKILL.mdcore12,657 bytesSKILL.mdcore12,657 bytesSKILL.mdcore12,657 bytesapi.pyruns7,973 bytesclinical_trial_finder.pyruns10,819 bytesconstants.pyruns7,705 bytesdemo.shruns3,540 bytesdemo_input.txtdoc892 byteseuctr.pyruns4,595 bytesexamples/README.mddoc2,196 bytesexamples/demo_output/checksums.sha256asset575 bytesexamples/demo_output/commands.shruns148 bytesexamples/demo_output/fhir_bundle.jsonasset44,464 bytesexamples/demo_output/figures/phase_distribution.pngasset48,991 bytesexamples/demo_output/report.htmlasset22,522 bytesexamples/demo_output/report.mddoc15,091 bytesexamples/demo_output/summary.jsonasset21,466 bytesexamples/demo_output/tables/trials.csvasset6,248 bytesgwas_bridge.pyruns7,594 bytesopentargets.pyruns3,439 bytestests/test_clinical_trial_finder.pyruns58,440 bytestests/test_fhir_e2e.pyruns13,217 bytestests/test_gwas_bridge_v2.pyruns4,706 byteswriters.pyruns26,214 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclinical-variant-prioritizer
When your agent uses it
Screen a genotype set (array or WGS-derived) against OMIM-morbid, ACMG-SF and Hereditary-Cancer gene panels and prioritise carried variants by ClinVar significance, gnomAD frequency, inheritance model and zygosity, following the pathogenicity-screening method of Corpas et al. 2021 (Whole Genome Interpretation for a Family of Five).
What it loads into context
Frontmatter
280 tokensAlways available to the agent
SKILL.md
996 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why it is not a raw ClinVar lookup
- Interface
- Panel
- Limitations
- Test
Scripts executed separately
api.pyprioritize.pytests/test_api.py
Files
SKILL.mdcore3,848 bytesSKILL.mdcore3,848 bytesSKILL.mdcore3,848 bytesapi.pyruns2,335 bytesprioritize.pyruns6,523 bytestests/test_api.pyruns3,517 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclinical-variant-reporter
When your agent uses it
Classify germline variants from VCF/BCF files according to the ACMG/AMP 2015 28-criteria evidence framework and generate clinical-grade interpretation reports with per-variant evidence audit trails and ACMG SF v3.2 secondary findings screening.
What it loads into context
Frontmatter
290 tokensAlways available to the agent
SKILL.md
4,186 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyacmg_engine.pyclinical_variant_reporter.pyself_audit.pytests/__init__.pytests/test_clinical_variant_reporter.pytests/test_self_audit.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesSKILL.mdcore16,594 bytesacmg_engine.pyruns24,539 bytesclinical_variant_reporter.pyruns41,062 bytesexample_data/demo_evidence_cache.jsonasset11,415 bytesexample_data/giab_acmg_panel.vcfasset2,818 bytesself_audit.pyruns9,542 bytestests/__init__.pyruns34 bytestests/test_clinical_variant_reporter.pyruns67,580 bytestests/test_self_audit.pyruns7,714 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubclinpgx
When your agent uses it
Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
What it loads into context
Frontmatter
127 tokensAlways available to the agent
SKILL.md
1,075 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Input Formats
- Workflow
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
Scripts executed separately
api.pyclinpgx.pytests/__init__.pytests/test_clinpgx.py
Files
INTENTS.jsonasset1,923 bytesSKILL.mdcore4,212 bytesSKILL.mdcore4,212 bytesSKILL.mdcore4,212 bytesapi.pyruns3,244 bytesclinpgx.pyruns26,322 bytestests/__init__.pyruns0 bytestests/test_clinpgx.pyruns15,930 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubcnv-acmg-classifier
When your agent uses it
Classify structural variants / copy-number variants (deletions and duplications) using the ClinGen / ACMG 2019 (Riggs et al. 2020) point framework and return a five-tier classification with a per-section evidence trail. Germline CNV interpretation, not SNV/indel.
What it loads into context
Frontmatter
598 tokensAlways available to the agent
SKILL.md
4,258 tokensWhen the skill is activated
Reference documents
643 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
- Self-Audit (SKILL.md Conformance Checklist)
Scripts executed separately
../../clawbio.pycnv_acmg_classifier.pytests/test_cnv_acmg_classifier.py
Files
../../clawbio.pyruns735 bytesINTENTS.jsonasset680 bytesSKILL.mdcore15,517 bytesSKILL.mdcore15,517 bytesSKILL.mdcore15,517 bytesSKILL.mdcore15,517 bytesSKILL.mdcore15,517 bytescnv_acmg_classifier.pyruns22,181 bytesdata/curated_dosage_map.csvasset327 bytesdata/curated_gene_model.csvasset1,693 bytesdemo_cnv_calls.csvasset432 bytesexamples/expected_classifications.csvasset612 bytesexamples/expected_demo_report.mddoc1,742 bytestests/test_cnv_acmg_classifier.pyruns17,346 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubcrispr-screen-triage
When your agent uses it
Deterministic CRISPR screen hit ranking from local guide-level count tables
What it loads into context
Frontmatter
339 tokensAlways available to the agent
SKILL.md
1,719 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Chaining Partners
- Maintenance
- Author & Attribution
- Citations
Scripts executed separately
../../clawbio.pycrispr_screen_triage.pytests/test_crispr_screen_triage.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore7,006 bytesSKILL.mdcore7,006 bytesSKILL.mdcore7,006 bytesSKILL.mdcore7,006 bytesSKILL.mdcore7,006 bytescrispr_screen_triage.pyruns8,904 bytesdemo_screen_counts.csvasset462 bytestests/test_crispr_screen_triage.pyruns5,335 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubdata-extractor
When your agent uses it
Extract numerical data from scientific figure images using Claude vision + OpenCV calibration. Supports 26+ plot types including bar charts, scatter plots, forest plots, Kaplan-Meier curves, box plots, and more.
What it loads into context
Frontmatter
223 tokensAlways available to the agent
SKILL.md
796 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- When to Use This Skill
- Capabilities
- Usage
- Input Formats
- Notes
Scripts executed separately
data_extractor.pydata_extractor_api.pydata_extractor_core/__init__.pydata_extractor_core/cv_calibration.pydata_extractor_core/digitizer.pydata_extractor_core/models.pytests/test_extractor.pyweb/app.jsweb/server.py
Files
SKILL.mdcore3,221 bytesSKILL.mdcore3,221 bytesSKILL.mdcore3,221 bytesSKILL.mdcore3,221 bytesdata_extractor.pyruns2,766 bytesdata_extractor_api.pyruns3,489 bytesdata_extractor_core/__init__.pyruns66 bytesdata_extractor_core/cv_calibration.pyruns13,654 bytesdata_extractor_core/digitizer.pyruns106,536 bytesdata_extractor_core/models.pyruns2,312 bytesrequirements.txtdoc16 bytestests/test_extractor.pyruns5,459 bytesweb/app.jsruns87,397 bytesweb/index.htmlasset4,874 bytesweb/server.pyruns10,524 bytesweb/styles.cssasset4,319 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubde-summary
When your agent uses it
Summarise pre-computed differential expression results with ranked gene lists, biological themes, and publication-ready interpretation.
What it loads into context
Frontmatter
359 tokensAlways available to the agent
SKILL.md
1,891 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Trigger
- Scope
- Workflow
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
Files
SKILL.mdcore8,036 bytesSKILL.mdcore8,036 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubdeepspot-m
When your agent uses it
Transcriptome-wide virtual spatial transcriptomics from H&E histology with DeepSpot-M. Scores a 224x224 tile and returns per-gene log1p-CPM values for any HGNC symbols you ask for, with a CSV, a report and a reproducibility bundle.
What it loads into context
Frontmatter
629 tokensAlways available to the agent
SKILL.md
6,546 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Chaining Partners
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pydeepspot_m.pytests/test_deepspot_m.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesSKILL.mdcore26,900 bytesdeepspot_m.pyruns37,597 bytesexamples/demo_expression.jsonasset527 bytesexamples/demo_tile.pngasset82,302 bytesrequirements.txtdoc364 bytestests/test_deepspot_m.pyruns37,303 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubdiff-visualizer
When your agent uses it
Rich downstream visualisation and reporting for bulk RNA-seq differential expression and scRNA marker/contrast outputs.
What it loads into context
Frontmatter
241 tokensAlways available to the agent
SKILL.md
1,665 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Output Structure
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pydiff_visualizer.pytests/test_diff_visualizer.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore6,486 bytesSKILL.mdcore6,486 bytesSKILL.mdcore6,486 bytesSKILL.mdcore6,486 bytesSKILL.mdcore6,486 bytesdiff_visualizer.pyruns86,496 bytesexamples/demo_bulk_counts.csvasset339 bytesexamples/demo_bulk_de_results.csvasset339 bytesexamples/demo_bulk_metadata.csvasset155 bytesexamples/demo_scrna_contrast.csvasset305 bytesexamples/demo_scrna_markers.csvasset271 bytestests/test_diff_visualizer.pyruns15,396 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubdnasp
When your agent uses it
Population genetics of pre-aligned DNA sequences or multi-sample VCFs using selected DnaSP 6 methods. Use for diversity, neutrality statistics, linkage disequilibrium, InDel polymorphism, divergence, MK, Ka/Ks and codon usage; not alignment, phasing or clinical interpretation.
What it loads into context
Frontmatter
2,021 tokensAlways available to the agent
SKILL.md
5,304 tokensWhen the skill is activated
Reference documents
8,676 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Scope
- Core Capabilities
- Workflow
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Known Differences from DnaSP 6.12.03
- Version History
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Chaining Partners
- Maintenance
Scripts executed separately
dnasp.pyenvironment.ymltests/test_clawbio_intents.pytests/test_coalescent_pvalues.pytests/test_dnasp.pytests/test_historical_comparisons.pytests/test_release_regressions.pytests/test_skill_contract.pytests/test_validation5_regressions.pytests/test_windows_encoding.py
Files
CONTRIBUTORS.mddoc1,050 bytesINTENTS.jsonasset834 bytesSKILL.mdcore20,388 bytesSKILL.mdcore20,388 bytesSKILL.mdcore20,388 bytesSKILL.mdcore20,388 bytesSKILL.mdcore20,388 bytesdnasp.pyruns273,996 bytesdocs/index.mddoc24,060 bytesdocs/version_history.mddoc4,944 bytesenvironment.ymlruns187 bytesexamples/demo_rp49.fasasset5,533 bytesexamples/demo_simple.fasasset132 bytestests/fixtures/historical_comparisons.jsonasset35,148 bytestests/fixtures/inputs/COII_Apes.nexasset21,502 bytestests/fixtures/inputs/COII_Apes_HsaPtr_pops.txtdoc121 bytestests/fixtures/inputs/COII_HsaPtr_outPpy.fasasset8,424 bytestests/fixtures/inputs/COII_Hsa_outPpy.fasasset4,914 bytestests/fixtures/inputs/COII_coding_1_681.fasasset8,256 bytestests/fixtures/inputs/DmelOSRegion.nexasset243,558 bytestests/fixtures/inputs/Ex_n1.fasasset323 bytestests/fixtures/inputs/README.mddoc2,489 bytestests/fixtures/inputs/hka_synthetic.tsvasset323 bytestests/fixtures/inputs/indel_help.fasasset303 bytestests/fixtures/inputs/ld_help.fasasset104 bytestests/fixtures/inputs/rp49_36.nexasset100,141 bytestests/fixtures/inputs/rp49_36_pops.txtdoc399 bytestests/fixtures/inputs/rp49_5regions/Region_1.fasasset1,380 bytestests/fixtures/inputs/rp49_5regions/Region_2.fasasset468 bytestests/fixtures/inputs/rp49_5regions/Region_3.fasasset696 bytestests/fixtures/inputs/rp49_5regions/Region_4.fasasset202 bytestests/fixtures/inputs/rp49_5regions/Region_5.fasasset752 bytestests/fixtures/inputs/rp49_ing34_outGUA.fasasset64,287 bytestests/fixtures/inputs/stop_family.fasasset56 bytestests/fixtures/inputs/vcf/Data_Example_DiploidPhased.vcfasset8,121 bytestests/fixtures/inputs/vcf/Data_Example_DiploidUnphased.vcfasset8,121 bytestests/fixtures/inputs/vcf/Data_Example_Haploid.vcfasset4,778 bytestests/fixtures/inputs/vcf/Data_Example_vcf.SG.txtdoc244 bytestests/fixtures/validation5/A2_rp49_win100_25.outasset5,179 bytestests/fixtures/validation5/C3_COII_win100_50.outasset2,861 bytestests/fixtures/validation5/E2_Dmel_win500_250.outasset3,441 bytestests/fixtures/validation5/M_ENC_standard_GUI_tables_transcribed.txtdoc3,189 bytestests/fixtures/validation5/M_ENC_vertebrate-mitochondrial_GUI_tables_transcribed.txtdoc3,827 bytestests/fixtures/validation5/README.mddoc1,807 bytestests/test_clawbio_intents.pyruns1,685 bytestests/test_coalescent_pvalues.pyruns23,055 bytestests/test_dnasp.pyruns166,221 bytestests/test_historical_comparisons.pyruns8,955 bytestests/test_release_regressions.pyruns14,488 bytestests/test_skill_contract.pyruns6,371 bytestests/test_validation5_regressions.pyruns24,040 bytestests/test_windows_encoding.pyruns2,868 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubdrug-photo
When your agent uses it
Medication photo to personalised PGx dosage card via Claude vision — snap a pill, get genotype-informed guidance
What it loads into context
Frontmatter
156 tokensAlways available to the agent
SKILL.md
1,459 tokensWhen the skill is activated
Reference documents
449 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Workflow
- Supported Drugs (51)
- Classification Labels
- CLI Reference
- Demo
- Output Structure
- Dependencies
- Safety
- Telegram Integration
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.py../pharmgx-reporter/pharmgx_reporter.py../pharmgx-reporter/pharmgx_reporter.py../pharmgx-reporter/pharmgx_reporter.py../pharmgx-reporter/pharmgx_reporter.py../pharmgx-reporter/pharmgx_reporter.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore5,517 bytesSKILL.mdcore5,517 bytesSKILL.mdcore5,517 bytesSKILL.mdcore5,517 bytesdemo-images/00-00-warfarin.jpgasset19,540 bytesdemo-images/00-01-warfarin.jpgasset57,971 bytesdemo-images/00-02-warfarin.jpgasset71,434 bytesdemo-images/00-03-warfarin.jpgasset8,599 bytesdemo-images/INDEX.mddoc1,601 bytesdemo-images/clopidogrel.jpgasset101,758 bytesdemo-images/codeine.jpgasset66,649 bytesdemo-images/fluoxetine.jpgasset30,094 bytesdemo-images/metoprolol.jpgasset175,336 bytesdemo-images/omeprazole.jpgasset76,552 bytesdemo-images/sertraline.jpgasset55,433 bytesdemo-images/simvastatin.jpgasset72,851 bytesdemo-images/tacrolimus.jpgasset24,175 bytesdemo-images/tamoxifen.jpgasset10,769 bytesdemo-images/warfarin.jpgasset34,840 bytes../pharmgx-reporter/pharmgx_reporter.pyruns99,535 bytes../pharmgx-reporter/pharmgx_reporter.pyruns99,535 bytes../pharmgx-reporter/pharmgx_reporter.pyruns99,535 bytes../pharmgx-reporter/pharmgx_reporter.pyruns99,535 bytes../pharmgx-reporter/pharmgx_reporter.pyruns99,535 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubdrug-repurposing-screen
When your agent uses it
Objective-driven pooled viability screen analysis: QC, hit calling, context-selectivity, biomarker sweep, and ranked repurposing candidates. Format-agnostic via schema.yaml + objective.yaml; includes offline demo.
What it loads into context
Frontmatter
765 tokensAlways available to the agent
SKILL.md
4,749 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pydrug_repurposing_screen.pygenerate_demo_bundle.pyscreen_engine.pytests/__init__.pytests/test_drug_repurposing_screen.pytests/test_generate_demo_bundle.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore19,428 bytesSKILL.mdcore19,428 bytesSKILL.mdcore19,428 bytesSKILL.mdcore19,428 bytesSKILL.mdcore19,428 bytesSKILL.mdcore19,428 bytesdemo/features/expression.csvasset5,961 bytesdemo/features/methylation.csvasset4,315 bytesdemo/manifest.jsonasset268 bytesdemo/metadata/sample_info.csvasset1,043 bytesdemo/metadata/treatment_info.csvasset4,745 bytesdemo/objective.yamlasset434 bytesdemo/readouts/primary.csvasset12,352 bytesdemo/schema.yamlasset561 bytesdrug_repurposing_screen.pyruns6,891 bytesgenerate_demo_bundle.pyruns8,238 bytesscreen_engine.pyruns25,294 bytestests/__init__.pyruns0 bytestests/test_drug_repurposing_screen.pyruns8,326 bytestests/test_generate_demo_bundle.pyruns2,172 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubena-fetch
When your agent uses it
Query metadata and download sequencing data from the European Nucleotide Archive (ENA) via the Portal and Browser APIs. Works with ENA/SRA accessions (PRJEB/PRJNA studies, ERR/SRR/DRR runs, ERX/SRX experiments, SAMEA/SAMN samples), listing runs and FASTQ links, building custom file reports, running advanced metadata searches, and emitting a standardised metadata.tsv plus a pipeline-ready nf-core/rnaseq or nf-core/scrnaseq samplesheet.csv.
What it loads into context
Frontmatter
752 tokensAlways available to the agent
SKILL.md
5,336 tokensWhen the skill is activated
Reference documents
5,233 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyena_fetch.pyena_fetch_api.pytests/test_ena_fetch.py
Files
../../clawbio.pyruns735 bytes../../docs/data-handling.mddoc19,645 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesSKILL.mdcore19,716 bytesena_fetch.pyruns15,077 bytesena_fetch_api.pyruns29,285 bytesexamples/demo_PRJEB56029_filereport.tsvasset5,026 bytesexamples/demo_sample_xml.jsonasset9,218 bytestests/test_ena_fetch.pyruns17,234 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubeqtl-catalogue-region-fetch
When your agent uses it
Fetch a region of cis-eQTL summary statistics from EBI eQTL Catalogue v7+ via tabix-on-FTP. Use when an agent needs eQTL beta / SE / p-value for every variant in a window around a gene's TSS for one specific dataset (study × tissue × quantification method). Input: dataset_id, chromosome, start, end, optional molecular_trait_id. Output: harmonised TSV slice.
What it loads into context
Frontmatter
747 tokensAlways available to the agent
SKILL.md
5,626 tokensWhen the skill is activated
Reference documents
519 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- Trigger
- Scope
- Workflow
- CLI Reference
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Citations
Scripts executed separately
../../clawbio.pyeqtl_catalogue_region_fetch.pyexamples/run_example.shtests/conftest.pytests/test_eqtl_catalogue_region_fetch.pytests/test_live_eqtl_catalogue_region_fetch.py
Files
../../clawbio.pyruns735 bytes.gitignoreasset245 bytesLICENSEasset1,067 bytesSKILL.mdcore21,216 bytesSKILL.mdcore21,216 bytesSKILL.mdcore21,216 bytesSKILL.mdcore21,216 bytesSKILL.mdcore21,216 bytesdata/dataset_index_r7.provenance.jsonasset5,381 bytesdata/dataset_index_r7.tsvasset66,786 bytesenvironment.ymlasset166 byteseqtl_catalogue_region_fetch.pyruns50,164 bytesexamples/default.jsonasset310 bytesexamples/expected_output.mddoc1,686 bytesexamples/il6r_gtex_small_intestine.jsonasset346 bytesexamples/input.jsonasset144 bytesexamples/irf5_gtex_adipose_visceral.jsonasset287 bytesexamples/run_example.shruns1,071 bytesexamples/sort1_gtex_minor_salivary_gland.jsonasset310 bytestests/conftest.pyruns659 bytestests/test_eqtl_catalogue_region_fetch.pyruns39,197 bytestests/test_live_eqtl_catalogue_region_fetch.pyruns3,481 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubequity-scorer
When your agent uses it
Compute HEIM diversity and equity metrics from VCF or ancestry data. Generates heterozygosity, FST, PCA plots, and a composite HEIM Equity Score with markdown reports.
What it loads into context
Frontmatter
181 tokensAlways available to the agent
SKILL.md
1,806 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Input Formats
- HEIM Equity Score Methodology
- Workflow
- Example Queries
- Output Structure
- Example Report Output
- Dependencies
- Safety
Scripts executed separately
api.pyequity_scorer.pytests/test_equity_scorer.pytests/test_repro_bundle.py
Files
SKILL.mdcore6,995 bytesSKILL.mdcore6,995 bytesSKILL.mdcore6,995 bytesapi.pyruns3,151 bytesequity_scorer.pyruns44,748 bytestests/test_equity_scorer.pyruns16,876 bytestests/test_repro_bundle.pyruns7,702 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubfastreer
When your agent uses it
Phylogenetic distance matrices and trees from VCF or FASTA data using the fastreeR hybrid Java/Python toolkit (VCF2TREE, VCF2DIST, DIST2TREE, FASTA2DIST).
What it loads into context
Frontmatter
703 tokensAlways available to the agent
SKILL.md
3,860 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyfastreer.pytests/test_fastreer.py
Files
../../clawbio.pyruns735 bytesINTENTS.jsonasset700 bytesSKILL.mdcore14,084 bytesSKILL.mdcore14,084 bytesSKILL.mdcore14,084 bytesSKILL.mdcore14,084 bytesSKILL.mdcore14,084 bytesSKILL.mdcore14,084 bytesSKILL.mdcore14,084 bytesexamples/demo_samples.vcfasset1,338 bytesexamples/demo_sequences.fastaasset350 bytesfastreer.pyruns24,303 bytestests/test_fastreer.pyruns5,769 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubfine-mapping
When your agent uses it
Statistical fine-mapping of GWAS loci using SuSiE, SuSiE-inf, and Approximate Bayes Factors to identify credible sets and posterior inclusion probabilities (PIPs) for causal variant discovery. SuSiE-inf adds an infinitesimal polygenic component for improved calibration at well-powered loci.
What it loads into context
Frontmatter
351 tokensAlways available to the agent
SKILL.md
4,061 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Gotchas
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
core/__init__.pycore/abf.pycore/credible_sets.pycore/io.pycore/report.pycore/susie.pycore/susie_inf.pyfine_mapping.pyfine_mapping_core/__init__.pyfine_mapping_core/abf.pyfine_mapping_core/credible_sets.pyfine_mapping_core/io.pyfine_mapping_core/report.pyfine_mapping_core/susie.pyfine_mapping_core/susie_inf.pytests/test_fine_mapping.py
Files
SKILL.mdcore14,730 bytesSKILL.mdcore14,730 bytesSKILL.mdcore14,730 bytesSKILL.mdcore14,730 bytesSKILL.mdcore14,730 bytesSKILL.mdcore14,730 bytescore/__init__.pyruns0 bytescore/abf.pyruns2,344 bytescore/credible_sets.pyruns5,499 bytescore/io.pyruns6,016 bytescore/report.pyruns22,125 bytescore/susie.pyruns8,861 bytescore/susie_inf.pyruns13,456 bytesfine_mapping.pyruns15,461 bytesfine_mapping_core/__init__.pyruns0 bytesfine_mapping_core/abf.pyruns2,344 bytesfine_mapping_core/credible_sets.pyruns5,499 bytesfine_mapping_core/io.pyruns6,016 bytesfine_mapping_core/report.pyruns22,125 bytesfine_mapping_core/susie.pyruns8,861 bytesfine_mapping_core/susie_inf.pyruns13,456 bytestests/fixtures/demo_susie_known_answer.jsonasset1,567 bytestests/test_fine_mapping.pyruns54,454 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubflow-bio
When your agent uses it
Flow.bio API bridge — authenticate, browse pipelines/samples/projects, search, upload data, launch pipeline executions, and check run status on any Flow instance.
What it loads into context
Frontmatter
472 tokensAlways available to the agent
SKILL.md
2,335 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyflow_bio.pytests/__init__.pytests/test_flow_bio.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore9,309 bytesSKILL.mdcore9,309 bytesSKILL.mdcore9,309 bytesSKILL.mdcore9,309 bytesSKILL.mdcore9,309 bytesSKILL.mdcore9,309 bytesdata/demo_cache.jsonasset26,339 bytesflow_bio.pyruns64,621 bytestests/__init__.pyruns0 bytestests/test_flow_bio.pyruns14,881 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgalaxy-bridge
When your agent uses it
Galaxy tool discovery, intelligent recommendation, and execution — 8,000+ bioinformatics tools from usegalaxy.org with multi-signal scoring and workflow suggestions
What it loads into context
Frontmatter
243 tokensAlways available to the agent
SKILL.md
2,489 tokensWhen the skill is activated
Reference documents
43,996 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Recommendation Engine
- Demo
- Galaxy Tool Categories
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
demo/reproducibility/commands.shgalaxy_bridge.pygenerate_curated_skills.pygenerate_galaxy_catalog.pytests/__init__.pytests/test_galaxy_bridge.pytests/test_tool_recommender.pytool_recommender.py
Files
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bytesgalaxy_skills/trinotate.mddoc559 bytesgalaxy_skills/tximport.mddoc551 bytesgalaxy_skills/umi-tools-count.mddoc625 bytesgalaxy_skills/umi-tools-deduplicate.mddoc619 bytesgalaxy_skills/umi-tools-extract.mddoc623 bytesgalaxy_skills/umi-tools-whitelist.mddoc649 bytesgalaxy_skills/vcf-to-maf-custom-track.mddoc448 bytesgalaxy_skills/velvetg.mddoc547 bytesgalaxy_skills/velveth.mddoc551 bytesgalaxy_skills/velvetoptimiser.mddoc614 bytesgalaxy_skills/vsearch-alignment.mddoc546 bytesgalaxy_skills/vsearch-chimera-detection.mddoc586 bytesgalaxy_skills/vsearch-clustering.mddoc551 bytesgalaxy_skills/vsearch-dereplication.mddoc566 bytesgalaxy_skills/vsearch-masking.mddoc536 bytesgalaxy_skills/vsearch-search.mddoc531 bytesgalaxy_skills/vsearch-shuffling.mddoc546 bytesgalaxy_skills/vsearch-sorting.mddoc536 bytesgalaxy_skills/winnowmap.mddoc638 bytesgenerate_curated_skills.pyruns8,381 bytesgenerate_galaxy_catalog.pyruns4,373 bytestests/__init__.pyruns0 bytestests/test_galaxy_bridge.pyruns10,503 bytestests/test_tool_recommender.pyruns12,997 bytestool_recommender.pyruns36,020 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgenome-compare
When your agent uses it
Compare your genome to George Church (PGP-1) and estimate ancestry composition via IBS and EM admixture
What it loads into context
Frontmatter
171 tokensAlways available to the agent
SKILL.md
1,268 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Reference Genome
- Workflow
- CLI Reference
- Demo
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.py__init__.pyapi.pygenome_compare.pytests/test_genome_compare.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore5,146 bytesSKILL.mdcore5,146 bytesSKILL.mdcore5,146 bytesSKILL.mdcore5,146 bytesSKILL.mdcore5,146 bytes__init__.pyruns31 bytesapi.pyruns2,611 bytesdata/aims_panel.jsonasset9,344 bytesdata/george_church_23andme.txt.gzasset4,993,370 bytesdata/manuel_ancestry.jsonasset1,311 bytesdata/manuel_corpas_23andme.txt.gzasset5,030,091 bytesgenome_compare.pyruns37,168 bytestests/test_genome_compare.pyruns11,157 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgenome-match
When your agent uses it
Score genetic compatibility across all male-female pairings in a Genomebook generation
What it loads into context
Frontmatter
166 tokensAlways available to the agent
SKILL.md
700 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Purpose
- How It Works
- Input
- Output
- CLI Usage
- Output Format
Scripts executed separately
genome_match.py
Files
SKILL.mdcore2,614 bytesSKILL.mdcore2,614 bytesSKILL.mdcore2,614 bytesgenome_match.pyruns3,513 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgeo-fetch
When your agent uses it
Query metadata and download data from the NCBI Gene Expression Omnibus (GEO). Works with GEO accessions (GSE series, GSM samples, GPL platforms, GDS datasets) to search GEO DataSets, fetch series and sample metadata, list and download series matrix / SOFT / MINiML / supplementary files, fetch the SRA Run Selector files, and emit a standardised metadata.tsv plus a pipeline-ready nf-core/rnaseq or nf-core/scrnaseq samplesheet.csv.
What it loads into context
Frontmatter
677 tokensAlways available to the agent
SKILL.md
5,091 tokensWhen the skill is activated
Reference documents
5,233 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pygeo_fetch.pygeo_fetch_api.pytests/test_geo_fetch.py
Files
../../clawbio.pyruns735 bytes../../docs/data-handling.mddoc19,645 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesSKILL.mdcore18,999 bytesexamples/demo_GSE30720_http.json.gzasset12,124 bytesgeo_fetch.pyruns10,822 bytesgeo_fetch_api.pyruns40,071 bytestests/test_geo_fetch.pyruns18,174 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgi-annotation
When your agent uses it
Predict gene and transcript structure (intervals, exons, strand) from a DNA sequence using the Genomic Intelligence DNA Annotation model, via the hosted /v1/tasks/annotation/predict API. Submitted asynchronously — the pipeline takes ~20 s for ~20 kbp.
What it loads into context
Frontmatter
544 tokensAlways available to the agent
SKILL.md
2,059 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- API Backed
- Workflow
- CLI Reference
- Authentication
- Demo
- Gotchas
- Output Structure
- Integration with Bio Orchestrator
- Safety
Scripts executed separately
../../clawbio.pyapi.pygi_annotation.pytests/__init__.pytests/test_gi_annotation.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesSKILL.mdcore8,445 bytesapi.pyruns1,359 bytesexample_data/annotation_tp53.faasset19,430 bytesgi_annotation.pyruns771 bytestests/__init__.pyruns0 bytestests/test_gi_annotation.pyruns1,435 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgi-chromatin
When your agent uses it
Predict chromatin state — histone marks, DNase, TF binding — across 919 tracks (DeepSEA-style) for DNA sequences, via the hosted Genomic Intelligence /v1/tasks/chromatin/predict API.
What it loads into context
Frontmatter
536 tokensAlways available to the agent
SKILL.md
1,890 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- API Backed
- Workflow
- CLI Reference
- Authentication
- Demo
- Gotchas
- Output Structure
- Integration with Bio Orchestrator
- Safety
Scripts executed separately
../../clawbio.pyapi.pygi_chromatin.pytests/__init__.pytests/test_gi_chromatin.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesSKILL.mdcore7,293 bytesapi.pyruns1,125 bytesexample_data/chromatin_active_promoter_chr19.faasset40,540 bytesgi_chromatin.pyruns550 bytestests/__init__.pyruns0 bytestests/test_gi_chromatin.pyruns1,515 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgi-enhancer
When your agent uses it
Predict enhancer activity in DNA sequences using the Genomic Intelligence G0 DeepSTARR model, via the hosted /v1/tasks/enhancer/predict API. Returns per-window activity scores.
What it loads into context
Frontmatter
534 tokensAlways available to the agent
SKILL.md
1,897 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- API Backed
- Workflow
- CLI Reference
- Authentication
- Demo
- Gotchas
- Output Structure
- Integration with Bio Orchestrator
- Safety
Scripts executed separately
../../clawbio.pyapi.pygi_enhancer.pytests/__init__.pytests/test_gi_enhancer.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesSKILL.mdcore7,446 bytesapi.pyruns1,122 bytesexample_data/enhancer_eve.faasset10,232 bytesgi_enhancer.pyruns525 bytestests/__init__.pyruns0 bytestests/test_gi_enhancer.pyruns1,455 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgi-expression
When your agent uses it
Predict tissue / cell-type expression (log TPM + TPM) from 9,198–500,000 bp of DNA around a TSS, at least 4,599 bp each side (anything but exactly 9,198 bp needs --tss-index) using the Genomic Intelligence G0 Expression model, via the hosted /v1/tasks/expression/predict API. The model is conditioned on a free-text cell-type / assay description.
What it loads into context
Frontmatter
616 tokensAlways available to the agent
SKILL.md
2,940 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- API Backed
- Workflow
- CLI Reference
- Authentication
- Demo
- Gotchas
- Output Structure
- Integration with Bio Orchestrator
- Safety
Scripts executed separately
../../clawbio.pyapi.pygi_expression.pytests/__init__.pytests/test_gi_expression.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesSKILL.mdcore11,799 bytesapi.pyruns1,609 bytesexample_data/expression_hbb_k562.faasset9,381 bytesgi_expression.pyruns917 bytestests/__init__.pyruns0 bytestests/test_gi_expression.pyruns5,361 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgi-promoter
When your agent uses it
Detect promoter regions in DNA sequences using the Genomic Intelligence G0 transformer (GENA-LM BERT Large), via the hosted /v1/tasks/promoter/predict API. Returns per-window promoter probabilities and called regions.
What it loads into context
Frontmatter
565 tokensAlways available to the agent
SKILL.md
2,585 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- API Backed
- Workflow
- CLI Reference
- Demo
- Authentication
- Gotchas
- Output Structure
- Integration with Bio Orchestrator
- Safety
Scripts executed separately
../../clawbio.pyapi.pygi_promoter.pytests/__init__.pytests/test_gi_promoter.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesSKILL.mdcore10,492 bytesapi.pyruns1,177 bytesexample_data/promoter_tp53.faasset26,276 bytesgi_promoter.pyruns517 bytestests/__init__.pyruns0 bytestests/test_gi_promoter.pyruns2,025 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgi-splice
When your agent uses it
Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.
What it loads into context
Frontmatter
558 tokensAlways available to the agent
SKILL.md
2,252 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- API Backed
- Workflow
- CLI Reference
- Demo
- Authentication
- Gotchas
- Output Structure
- Integration with Bio Orchestrator
- Safety
Scripts executed separately
../../clawbio.pyapi.pygi_splice.pytests/__init__.pytests/test_gi_splice.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesSKILL.mdcore8,991 bytesapi.pyruns1,116 bytesexample_data/splice_hbb.faasset4,048 bytesgi_splice.pyruns511 bytestests/__init__.pyruns0 bytestests/test_gi_splice.pyruns1,636 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgwas-catalog-region-fetch
When your agent uses it
Fetch a region of GWAS summary statistics from the NHGRI-EBI GWAS Catalog harmonised collection via tabix-on-FTP. Use when an agent needs GWAS beta / SE / p-value for every variant in a window for one specific study (GCST accession). Input: accession, chromosome, start, end. Output: harmonised TSV slice in canonical format.
What it loads into context
Frontmatter
578 tokensAlways available to the agent
SKILL.md
3,973 tokensWhen the skill is activated
Reference documents
221 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- Trigger
- Scope
- Workflow
- CLI Reference
- Output Structure
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Citations
Scripts executed separately
../../clawbio.pyexamples/run_example.shgwas_catalog_region_fetch.pytests/conftest.pytests/test_gwas_catalog_region_fetch.pytests/test_live_gwas_catalog_region_fetch.pytests/test_reproducibility_bundle.py
Files
../../clawbio.pyruns735 bytes.gitignoreasset245 bytesLICENSEasset1,067 bytesSKILL.mdcore15,010 bytesSKILL.mdcore15,010 bytesSKILL.mdcore15,010 bytesSKILL.mdcore15,010 bytesenvironment.ymlasset183 bytesexamples/default.jsonasset260 bytesexamples/expected_output.mddoc750 bytesexamples/il6r_crp.yamlasset296 bytesexamples/input.jsonasset103 bytesexamples/run_example.shruns879 bytesexamples/sort1_cholesterol_vldl.jsonasset260 bytesexamples/tcf7l2_hba1c.jsonasset252 bytesgwas_catalog_region_fetch.pyruns24,281 bytestests/conftest.pyruns961 bytestests/test_gwas_catalog_region_fetch.pyruns10,002 bytestests/test_live_gwas_catalog_region_fetch.pyruns1,408 bytestests/test_reproducibility_bundle.pyruns1,913 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgwas-lookup
When your agent uses it
Federated variant lookup across 8 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, and more.
What it loads into context
Frontmatter
141 tokensAlways available to the agent
SKILL.md
1,202 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Input Formats
- Databases Queried
- Workflow
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
Scripts executed separately
gwas_lookup.pygwas_lookup_api/__init__.pygwas_lookup_api/base_client.pygwas_lookup_api/ensembl.pygwas_lookup_api/finngen.pygwas_lookup_api/gtex.pygwas_lookup_api/gwas_catalog.pygwas_lookup_api/open_targets.pygwas_lookup_api/pheweb_bbj.pygwas_lookup_api/pheweb_ukb.pygwas_lookup_api/portaldev.pygwas_lookup_core/__init__.pygwas_lookup_core/normalise.pygwas_lookup_core/report.pygwas_lookup_core/resolve.pytests/__init__.pytests/test_base_client.pytests/test_gwas_catalog_v2.pytests/test_gwas_lookup.pytests/test_live_gwas_lookup.py
Files
INTENTS.jsonasset1,260 bytesSKILL.mdcore4,454 bytesSKILL.mdcore4,454 bytesSKILL.mdcore4,454 bytesdata/demo_rs3798220.jsonasset10,917 bytesgwas_lookup.pyruns14,032 bytesgwas_lookup_api/__init__.pyruns3,858 bytesgwas_lookup_api/base_client.pyruns5,360 bytesgwas_lookup_api/ensembl.pyruns3,925 bytesgwas_lookup_api/finngen.pyruns1,961 bytesgwas_lookup_api/gtex.pyruns2,183 bytesgwas_lookup_api/gwas_catalog.pyruns5,560 bytesgwas_lookup_api/open_targets.pyruns3,709 bytesgwas_lookup_api/pheweb_bbj.pyruns2,098 bytesgwas_lookup_api/pheweb_ukb.pyruns2,036 bytesgwas_lookup_api/portaldev.pyruns1,644 bytesgwas_lookup_core/__init__.pyruns27 bytesgwas_lookup_core/normalise.pyruns6,765 bytesgwas_lookup_core/report.pyruns14,529 bytesgwas_lookup_core/resolve.pyruns2,731 bytestests/__init__.pyruns0 bytestests/fixtures/ensembl_variation.jsonasset516 bytestests/fixtures/error_api.jsonasset82 bytestests/fixtures/gtex.jsonasset475 bytestests/fixtures/gwas_catalog.jsonasset1,231 bytestests/fixtures/gwas_catalog_legacy_410.txtdoc237 bytestests/fixtures/gwas_catalog_v2_rs2187668.jsonasset31,901 bytestests/fixtures/gwas_catalog_v2_rs7903146_page0.jsonasset395,957 bytestests/fixtures/gwas_catalog_v2_rs7903146_page1.jsonasset305,395 bytestests/fixtures/open_targets_credsets.jsonasset563 bytestests/fixtures/open_targets_platform_credsets.jsonasset1,275 bytestests/fixtures/pheweb_ukb.jsonasset648 bytestests/test_base_client.pyruns2,840 bytestests/test_gwas_catalog_v2.pyruns8,755 bytestests/test_gwas_lookup.pyruns15,358 bytestests/test_live_gwas_lookup.pyruns1,096 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgwas-pipeline
When your agent uses it
End-to-end GWAS automation wrapping PLINK2 for genotype QC and REGENIE for two-step whole-genome regression association testing. Produces Manhattan plots, QQ plots, clumped lead variants, and structured summary statistics.
What it loads into context
Frontmatter
281 tokensAlways available to the agent
SKILL.md
1,564 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyexample_data/example.bedexample_data/example.bimexample_data/example.famgwas_pipeline.pytests/__init__.pytests/test_gwas_pipeline.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore5,696 bytesSKILL.mdcore5,696 bytesSKILL.mdcore5,696 bytesexample_data/covariates.txtdoc31,020 bytesexample_data/example.bedruns125,003 bytesexample_data/example.bgenasset186,196 bytesexample_data/example.bimruns15,786 bytesexample_data/example.famruns16,613 bytesexample_data/phenotype_bin.txtdoc5,798 bytesexample_data/test_bin_out_firth_Y1.regenieasset72,452 bytesgwas_pipeline.pyruns28,165 bytestests/__init__.pyruns22 bytestests/test_gwas_pipeline.pyruns8,127 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgwas-prs
When your agent uses it
Calculate polygenic risk scores from DTC genetic data using the PGS Catalog
What it loads into context
Frontmatter
104 tokensAlways available to the agent
SKILL.md
3,471 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Input Formats
- Workflow
- Example Queries
- Output Structure
- Dependencies
- Scoring Model
- Reference Distributions
- PGS Catalog API
- Safety
- Integration with Bio Orchestrator
Scripts executed separately
api.pygenerate_curated_scores.pygwas_prs.pygwas_prs_repro_bundle.pytests/test_curated_panel_ids.pytests/test_gwas_prs.pytests/test_legacy_alias_opt_in.pytests/test_repro_bundle.pytests/test_score_provenance.py
Files
INTENTS.jsonasset668 bytesSKILL.mdcore13,892 bytesSKILL.mdcore13,892 bytesSKILL.mdcore13,892 bytesSKILL.mdcore13,892 bytesapi.pyruns5,778 bytescurated_scores.jsonasset2,793 bytesdata/CLAWBIO-AF-12_GRCh37.txtdoc1,477 bytesdata/CLAWBIO-BC-77_GRCh37.txtdoc3,898 bytesdata/CLAWBIO-BMI-97_GRCh37.txtdoc4,494 bytesdata/CLAWBIO-CAD-46_GRCh37.txtdoc2,711 bytesdata/CLAWBIO-PC-147_GRCh37.txtdoc6,340 bytesdata/CLAWBIO-T2D-8_GRCh37.txtdoc1,325 bytesdemo_patient_prs.txtdoc10,482 bytesgenerate_curated_scores.pyruns2,487 bytesgwas_prs.pyruns64,609 bytesgwas_prs_repro_bundle.pyruns8,558 bytestests/fixtures/mock_genotype_23andme.txtdoc202 bytestests/fixtures/mock_genotype_ancestry.txtdoc182 bytestests/fixtures/mock_score_metadata.jsonasset923 bytestests/fixtures/mock_scores_by_trait.jsonasset736 bytestests/fixtures/mock_scoring_file.txtdoc358 bytestests/fixtures/mock_trait_search.jsonasset240 bytestests/test_curated_panel_ids.pyruns7,626 bytestests/test_gwas_prs.pyruns14,234 bytestests/test_legacy_alias_opt_in.pyruns6,363 bytestests/test_repro_bundle.pyruns18,257 bytestests/test_score_provenance.pyruns14,591 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubgwas-sumstats-harmonize
When your agent uses it
Harmonize GWAS summary statistics from any common format (GWAS-Catalog SSF, PLINK 1.9/2, REGENIE, METAL, BOLT, SAIGE) to one canonical table (SNP CHR BP EA NEA EAF BETA SE P N): column detection, BETA/SE/P derivation, QC with drop reasons, and allele alignment to a reference panel, run as a Snakemake workflow.
What it loads into context
Frontmatter
666 tokensAlways available to the agent
SKILL.md
4,551 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyexamples/make_demo_data.pygwas_sumstats_harmonize.pytests/test_gwas_sumstats_harmonize.pyworkflow/config/config_loader.pyworkflow/scripts/align_reference.pyworkflow/scripts/derive_effects.pyworkflow/scripts/lib/harmonize_lib.pyworkflow/scripts/map_columns.pyworkflow/scripts/qc_filter.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore16,935 bytesSKILL.mdcore16,935 bytesSKILL.mdcore16,935 bytesSKILL.mdcore16,935 bytesSKILL.mdcore16,935 bytesexamples/cohort_metal.tblasset9,416 bytesexamples/cohort_plink2.glm.logisticasset12,296 bytesexamples/cohort_regenie.regenieasset12,084 bytesexamples/cohort_saige.txtdoc16,345 bytesexamples/cohort_ssf.tsvasset12,162 bytesexamples/demo_manifest.yamlasset669 bytesexamples/make_demo_data.pyruns6,352 bytesexamples/reference.tsvasset4,306 bytesgwas_sumstats_harmonize.pyruns22,021 bytestests/test_gwas_sumstats_harmonize.pyruns41,728 bytesworkflow/Snakefileasset2,188 bytesworkflow/config/config_loader.pyruns4,616 bytesworkflow/envs/python.yamlasset194 bytesworkflow/rules/align_reference.smkasset1,275 bytesworkflow/rules/common.smkasset292 bytesworkflow/rules/derive_effects.smkasset875 bytesworkflow/rules/map_columns.smkasset907 bytesworkflow/rules/qc_filter.smkasset1,155 bytesworkflow/scripts/align_reference.pyruns6,411 bytesworkflow/scripts/derive_effects.pyruns5,026 bytesworkflow/scripts/lib/harmonize_lib.pyruns13,838 bytesworkflow/scripts/map_columns.pyruns5,244 bytesworkflow/scripts/qc_filter.pyruns5,333 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubhla-typing
When your agent uses it
HLA allele typing from WGS/WES VCF data
What it loads into context
Frontmatter
319 tokensAlways available to the agent
SKILL.md
1,781 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyapi.pyhla_typing.pytests/test_hla_typing.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore7,174 bytesSKILL.mdcore7,174 bytesSKILL.mdcore7,174 bytesSKILL.mdcore7,174 bytesSKILL.mdcore7,174 bytesapi.pyruns626 bytesbench_test_cases/ht_01_basic_correct/ground_truth.txtdoc324 bytesbench_test_cases/ht_01_basic_correct/input.txtdoc148 bytesbench_test_cases/ht_02_empty_input/ground_truth.txtdoc335 bytesbench_test_cases/ht_02_empty_input/input.txtdoc67 bytesbench_test_cases/ht_03_malformed_input/ground_truth.txtdoc346 bytesbench_test_cases/ht_03_malformed_input/input.txtdoc119 bytesdemo_input.txtdoc291 byteshla_typing.pyruns4,861 bytestests/test_hla_typing.pyruns4,506 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubigv-validator
When your agent uses it
Read-level validation of variant calls from any VCF, tumor/normal or tumor-only: counts read support in the BAMs (SNVs, indels, SV breakpoints), compares it with the caller's reported counts, flags artifact patterns, takes one IGV screenshot per variant and writes a report.
What it loads into context
Frontmatter
830 tokensAlways available to the agent
SKILL.md
9,317 tokensWhen the skill is activated
Reference documents
6,578 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- Modes
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Step by step: validating a whole project
- Reading the summary: what to trust
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pydemo/make_demo_data.pyigv_validator.pytests/test_igv_validator.py
Files
../../clawbio.pyruns735 bytesGUIDE.mddoc19,144 bytesSKILL.mdcore35,077 bytesSKILL.mdcore35,077 bytesSKILL.mdcore35,077 bytesSKILL.mdcore35,077 bytesSKILL.mdcore35,077 bytesSKILL.mdcore35,077 bytesSKILL.mdcore35,077 bytesSKILL.mdcore35,077 bytesdemo/demo_calls.vcfasset1,288 bytesdemo/demo_cnv.tsvasset625 bytesdemo/demo_cnv_genes.bedasset222 bytesdemo/demo_normal.bamasset304,035 bytesdemo/demo_normal.bam.baiasset280 bytesdemo/demo_ref.faasset91,732 bytesdemo/demo_ref.fa.faiasset69 bytesdemo/demo_truth.jsonasset1,520 bytesdemo/demo_tumor.bamasset275,020 bytesdemo/demo_tumor.bam.baiasset280 bytesdemo/demo_variants.tsvasset132 bytesdemo/make_demo_data.pyruns16,214 bytesexamples/README.mddoc744 bytesexamples/curated_calls.csvasset132 bytesexamples/demo_report.mddoc3,450 bytesexamples/genes.bedasset269 bytesexamples/samples.csvasset319 bytesigv_validator.pyruns199,538 bytestests/test_igv_validator.pyruns113,071 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubillumina-bridge
When your agent uses it
Import DRAGEN-exported Illumina result bundles into ClawBio for local tertiary analysis and downstream routing.
What it loads into context
Frontmatter
213 tokensAlways available to the agent
SKILL.md
3,231 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Minimal ICA Maintainer Setup
- Algorithm / Methodology
- ICA v3 Result Contract
- ICA Error Handling
- Example Queries
- Output Structure
- Dependencies
- Safety
- Known Limits
- Testing
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyillumina_bridge.pyillumina_bundle.pyillumina_providers.pytests/test_illumina_bridge.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesSKILL.mdcore12,977 bytesdemo_bundle/SampleSheet.csvasset350 bytesdemo_bundle/demo.vcfasset272 bytesdemo_bundle/mock_ica_metadata.jsonasset364 bytesdemo_bundle/qc_metrics.jsonasset167 bytesillumina_bridge.pyruns17,663 bytesillumina_bundle.pyruns17,607 bytesillumina_providers.pyruns12,092 bytestests/test_illumina_bridge.pyruns28,902 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubjust-prs-mcp
When your agent uses it
Compute evidence-aware polygenic risk scores from a local VCF or WGS file through the validated just-prs engine and a pinned local just-prs MCP server.
What it loads into context
Frontmatter
476 tokensAlways available to the agent
SKILL.md
3,459 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Validation Evidence
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
just_prs_mcp_bridge.pymcp_client.pytests/test_just_prs_mcp.pytests/test_live_integration.py
Files
INTENTS.jsonasset720 bytesSKILL.mdcore14,027 bytesSKILL.mdcore14,027 bytesSKILL.mdcore14,027 bytesSKILL.mdcore14,027 bytesexamples/demo_patient.vcfasset313 bytesjust_prs_mcp_bridge.pyruns38,893 bytesmcp_client.pyruns3,652 bytestests/fixtures/demo_trait_report.jsonasset2,706 bytestests/test_just_prs_mcp.pyruns27,122 bytestests/test_live_integration.pyruns3,658 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHublabstep
When your agent uses it
Query and display Labstep electronic lab notebook data — experiments, protocols, resources, and inventory — via labstepPy. Supports offline demo mode with synthetic biology data.
What it loads into context
Frontmatter
219 tokensAlways available to the agent
SKILL.md
2,328 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Authentication
- Read-Only Policy
- Workflow
- Key Entity Methods
- CLI Reference
- Demo
- Output Structure
- Example Queries
- Common Patterns
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Notes
Scripts executed separately
labstep.pytests/test_labstep.py
Files
SKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesSKILL.mdcore9,277 bytesdemo/demo_experiments.jsonasset3,697 bytesdemo/demo_inventory.jsonasset4,490 bytesdemo/demo_protocols.jsonasset4,274 byteslabstep.pyruns20,234 bytestests/test_labstep.pyruns13,051 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubld-1000g-region-compute
When your agent uses it
Compute pairwise r² between a lead variant and every variant in a window using the 1000 Genomes Phase 3 GRCh38 reference panel, ancestry-stratified. Use when an agent needs LD coloring for a regional plot or LD pruning around a candidate causal variant. Single client (on-demand region fetch from EBI 1000G FTP); no multi-GB cold-start.
What it loads into context
Frontmatter
739 tokensAlways available to the agent
SKILL.md
4,355 tokensWhen the skill is activated
Reference documents
385 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- Trigger
- Scope
- Workflow
- CLI Reference
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Citations
Scripts executed separately
../../clawbio.pyexamples/run_example.shld_1000g_region_compute.pyondemand_client.pytests/conftest.pytests/test_ld_1000g_region_compute.pytests/test_live_ld_1000g_region_compute.py
Files
../../clawbio.pyruns735 bytes.gitignoreasset302 bytesLICENSEasset1,067 bytesSKILL.mdcore15,472 bytesSKILL.mdcore15,472 bytesSKILL.mdcore15,472 bytesenvironment.ymlasset231 bytesexamples/default.jsonasset234 bytesexamples/expected_output.mddoc1,125 bytesexamples/run_example.shruns1,060 bytesexamples/sort1_locus_eur.jsonasset234 bytesld_1000g_region_compute.pyruns12,408 bytesondemand_client.pyruns13,921 bytestests/conftest.pyruns987 bytestests/test_ld_1000g_region_compute.pyruns7,558 bytestests/test_live_ld_1000g_region_compute.pyruns2,041 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHublit-synthesizer
When your agent uses it
Search PubMed and bioRxiv for bioinformatics literature, synthesise results into a structured report, and build a citation graph — all locally, with a reproducibility bundle.
What it loads into context
Frontmatter
395 tokensAlways available to the agent
SKILL.md
2,749 tokensWhen the skill is activated
Reference documents
1,275 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyexamples/demo_sources/fetch_demo_sources.pylit_synthesizer.pytests/test_demo_provenance.pytests/test_lit_synthesizer.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore10,801 bytesSKILL.mdcore10,801 bytesSKILL.mdcore10,801 bytesSKILL.mdcore10,801 bytesSKILL.mdcore10,801 bytesexamples/demo_output/report.mddoc4,770 bytesexamples/demo_papers.jsonasset8,114 bytesexamples/demo_sources/biorxiv_details.jsonasset2,248 bytesexamples/demo_sources/fetch_demo_sources.pyruns2,928 bytesexamples/demo_sources/pubmed_efetch.xmlasset82,702 bytesexamples/demo_sources/pubmed_elink_refs.jsonasset2,824 byteslit_synthesizer.pyruns16,934 bytestests/test_demo_provenance.pyruns3,649 bytestests/test_lit_synthesizer.pyruns7,475 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHublocuscompare-region-render
When your agent uses it
Render a 4-panel regional LocusCompare diagnostic for one (lead variant, exposure study, outcome study) tuple - overlays GWAS Manhattan, QTL Manhattan, GENCODE gene track, and cross-trait scatter colored by LD r². Use when an agent needs visual confirmation that two GWAS / QTL signals share the same causal variant (the Liu 2019 LocusCompare convention). Inputs: lead variant + two pre-fetched harmonised sumstats slices (or eQTL Catalogue / GWAS Catalog identifiers for bundled fetch). Output: PNG + JSON manifest.
What it loads into context
Frontmatter
926 tokensAlways available to the agent
SKILL.md
6,806 tokensWhen the skill is activated
Reference documents
14,248 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Overview
- Trigger
- Scope
- Workflow
- CLI Reference
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Citations
Scripts executed separately
../../clawbio.py_fetchers/__init__.py_fetchers/gencode_ondemand.py_prefetched.py_region_harmonise.py_wald_ratio_types.pycli.pycommands.shexamples/01_synthetic_demo/generate_synthetic_fixtures.pyexamples/recipes/finngen_direct/harmonise.shexamples/recipes/gtex_v10_direct/harmonise.shexamples/recipes/pan_ukbb_direct/harmonise.shexamples/recipes/ukb_ppp_pqtl/harmonise.shlocuscompare_region_render.pyregional_plot.pytests/__init__.pytests/test_cli.pytests/test_effect_size_panel_odds_ratio.pytests/test_gencode_ondemand.pytests/test_gene_track_xlim.pytests/test_generate_synthetic_fixtures.pytests/test_golden_parity_sort1_dual_modality.pytests/test_live_locuscompare_region_render.pytests/test_locuscompare_region_render.pytests/test_pqtl_caption_n.pytests/test_prefetched.pytests/test_regional_plot.pytests/test_wald_ratio_types.py
Files
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No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubmarker-dominance-mapper
When your agent uses it
Deterministic marker-dominance region mapping from local spot-count CSVs
What it loads into context
Frontmatter
326 tokensAlways available to the agent
SKILL.md
1,584 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Chaining Partners
- Maintenance
- Author & Attribution
- Citations
Scripts executed separately
../../clawbio.pymarker_dominance_mapper.pytests/test_marker_dominance_mapper.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore6,566 bytesSKILL.mdcore6,566 bytesSKILL.mdcore6,566 bytesSKILL.mdcore6,566 bytesSKILL.mdcore6,566 bytesdemo_marker_counts.csvasset219 bytesmarker_dominance_mapper.pyruns9,844 bytestests/test_marker_dominance_mapper.pyruns5,213 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubmendelian-randomisation
When your agent uses it
Two-sample Mendelian Randomisation from GWAS summary statistics with IVW, MR-Egger, weighted median/mode, and full sensitivity analysis (Cochran Q, Egger intercept, Steiger, F-statistic, leave-one-out).
What it loads into context
Frontmatter
507 tokensAlways available to the agent
SKILL.md
4,690 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pymendelian_randomisation.pytests/__init__.pytests/test_mendelian_randomisation.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore18,234 bytesSKILL.mdcore18,234 bytesSKILL.mdcore18,234 bytesSKILL.mdcore18,234 bytesSKILL.mdcore18,234 bytesexample_data/demo_instruments.jsonasset11,835 bytesmendelian_randomisation.pyruns55,589 bytestests/__init__.pyruns32 bytestests/test_mendelian_randomisation.pyruns49,984 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubmethylation-clock
When your agent uses it
Compute epigenetic age from DNA methylation arrays using PyAging clocks from GEO accessions or local files.
What it loads into context
Frontmatter
244 tokensAlways available to the agent
SKILL.md
958 tokensWhen the skill is activated
Reference documents
266 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Domain Decisions
- Safety Rules
- Agent Boundary
Scripts executed separately
methylation_clock.pytests/test_methylation_clock.pytests/test_sha256_delegation.py
Files
SKILL.mdcore3,782 bytesSKILL.mdcore3,782 bytesSKILL.mdcore3,782 bytesSKILL.mdcore3,782 bytesSKILL.mdcore3,782 bytesdata/GSE139307_small.csv.gzasset5,845,000 bytesdata/PROVENANCE.mddoc1,077 bytesmethylation_clock.pyruns17,331 bytestests/test_methylation_clock.pyruns2,149 bytestests/test_sha256_delegation.pyruns812 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubmultiqc-reporter
When your agent uses it
Aggregates QC reports from any bioinformatics tool outputs (FastQC, fastp, STAR, Picard, samtools, etc.) into a single MultiQC HTML report plus a ClawBio markdown summary with per-sample QC metrics.
What it loads into context
Frontmatter
450 tokensAlways available to the agent
SKILL.md
2,522 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
multiqc_reporter.pytests/__init__.pytests/test_multiqc_reporter.py
Files
SKILL.mdcore9,717 bytesSKILL.mdcore9,717 bytesSKILL.mdcore9,717 bytesmultiqc_reporter.pyruns10,380 bytestests/__init__.pyruns0 bytestests/test_multiqc_reporter.pyruns5,130 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubncbi-datasets
When your agent uses it
Download genomes, genes, virus sequences, and taxonomy data from NCBI using the datasets and dataformat CLI tools.
What it loads into context
Frontmatter
322 tokensAlways available to the agent
SKILL.md
2,869 tokensWhen the skill is activated
Reference documents
3,928 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Workflow
- Input Formats
- CLI Reference
- Demo
- Downloaded ZIP file structure
- Dependencies
- Error handling
- Safety
- Citations
Files
SKILL.mdcore12,419 bytesSKILL.mdcore12,419 bytesSKILL.mdcore12,419 bytesSKILL.mdcore12,419 bytesSKILL.mdcore12,419 bytesreferences/ncbi-datasets.mddoc14,863 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubnfcore-rnaseq-wrapper
When your agent uses it
Wrapper skill for running nf-core/rnaseq bulk RNA-seq preprocessing from FASTQ or BAM inputs with strict preflight, reproducibility outputs, and downstream handoff to ClawBio bulk RNA-seq DE skills.
What it loads into context
Frontmatter
564 tokensAlways available to the agent
SKILL.md
9,243 tokensWhen the skill is activated
Reference documents
6,211 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Scope
- Why This Exists
- Core Capabilities
- Aligners
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Citations
Scripts executed separately
../../clawbio.py_isolated_imports.pycommand_builder.pyerrors.pyexecutor.pynfcore_rnaseq_wrapper.pyoutputs_parser.pyparams_builder.pypipeline_source.pypreflight.pyprovenance.pyremap_paths.pyreporting.pysamplesheet_builder.pyschemas.pytests/conftest.pytests/test_audit_rnaseq_hardening.pytests/test_bundle_portability.pytests/test_command_builder.pytests/test_drift_guards.pytests/test_error_codes.pytests/test_executor.pytests/test_nfcore_rnaseq_wrapper.pytests/test_outputs_parser.pytests/test_params_builder.pytests/test_pipeline_source.pytests/test_portability_remap_interpreter.pytests/test_preflight.pytests/test_provenance.pytests/test_remap_paths.pytests/test_reporting.pytests/test_samplesheet_builder.py
Files
../../clawbio.pyruns735 bytesCHANGELOG.mddoc24,535 bytesSKILL.mdcore36,010 bytesSKILL.mdcore36,010 bytesSKILL.mdcore36,010 bytesSKILL.mdcore36,010 bytesSKILL.mdcore36,010 bytesSKILL.mdcore36,010 bytes_isolated_imports.pyruns1,266 bytescommand_builder.pyruns3,023 bytesdemo/README.mddoc312 byteserrors.pyruns4,123 bytesexecutor.pyruns9,008 bytesnfcore_rnaseq_wrapper.pyruns73,708 bytesoutputs_parser.pyruns13,942 bytesparams_builder.pyruns13,659 bytespipeline_source.pyruns6,005 bytespreflight.pyruns85,016 bytesprovenance.pyruns15,291 bytesremap_paths.pyruns29,294 bytesreporting.pyruns26,351 bytesreproducibility/compatibility_policy.jsonasset1,453 bytesreproducibility/pinned_versions.jsonasset1,548 bytessamplesheet_builder.pyruns19,534 bytesschemas.pyruns5,747 bytestests/conftest.pyruns5,639 bytestests/test_audit_rnaseq_hardening.pyruns20,310 bytestests/test_bundle_portability.pyruns5,968 bytestests/test_command_builder.pyruns7,038 bytestests/test_drift_guards.pyruns6,123 bytestests/test_error_codes.pyruns5,765 bytestests/test_executor.pyruns12,944 bytestests/test_nfcore_rnaseq_wrapper.pyruns54,446 bytestests/test_outputs_parser.pyruns16,037 bytestests/test_params_builder.pyruns22,083 bytestests/test_pipeline_source.pyruns12,274 bytestests/test_portability_remap_interpreter.pyruns1,666 bytestests/test_preflight.pyruns78,558 bytestests/test_provenance.pyruns19,588 bytestests/test_remap_paths.pyruns31,367 bytestests/test_reporting.pyruns37,057 bytestests/test_samplesheet_builder.pyruns14,289 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubnfcore-rnastructurome-wrapper
When your agent uses it
Wrapper skill for running nf-core/rnastructurome — chemical-probing RNA structure analysis (SHAPE/DMS, RT-stop/MaP readout) from FASTQ to per-base reactivity, secondary-structure predictions, and 2D diagrams.
What it loads into context
Frontmatter
648 tokensAlways available to the agent
SKILL.md
6,809 tokensWhen the skill is activated
Reference documents
8,844 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Scope
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Citations
Files
README.mddoc1,422 bytesSKILL.mdcore26,667 bytesSKILL.mdcore26,667 bytesSKILL.mdcore26,667 bytesSKILL.mdcore26,667 bytesdemo/README.mddoc1,239 bytesreferences/parameters.mddoc29,578 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubnfcore-sarek-wrapper
When your agent uses it
ClawBio wrapper around nf-core/sarek 3.8.1 covering mapping through annotation for germline, tumor-only, and somatic paired analyses.
What it loads into context
Frontmatter
673 tokensAlways available to the agent
SKILL.md
10,749 tokensWhen the skill is activated
Reference documents
15,515 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Scope
- Why This Exists
- Core Capabilities
- Steps
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Citations
Scripts executed separately
../../clawbio.py_isolated_imports.pycommand_builder.pyerrors.pyexecutor.pynfcore_sarek_wrapper.pyoutputs_parser.pyparams_builder.pypipeline_source.pypreflight.pyprovenance.pyremap_paths.pyreporting.pysamplesheet_builder.pyschemas.pytests/conftest.pytests/preflight_fixtures.pytests/test_catalog_consistency.pytests/test_cli_direct_invocation.pytests/test_current_audit_regressions.pytests/test_executor.pytests/test_nfcore_sarek_wrapper.pytests/test_outputs_parser.pytests/test_params_builder.pytests/test_portability_remap_interpreter.pytests/test_preflight.pytests/test_provenance.pytests/test_remap_paths.pytests/test_reporting.pytests/test_samplesheet_builder.py
Files
../../clawbio.pyruns735 bytes.gitignoreasset569 bytesCHANGELOG.mddoc61,026 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytesSKILL.mdcore42,381 bytes_isolated_imports.pyruns1,266 bytescommand_builder.pyruns3,039 bytesdemo/README.mddoc346 byteserrors.pyruns4,976 bytesexecutor.pyruns8,942 bytesnfcore_sarek_wrapper.pyruns79,286 bytesoutputs_parser.pyruns52,236 bytesparams_builder.pyruns17,308 bytespipeline_source.pyruns2,845 bytespreflight.pyruns108,904 bytesprovenance.pyruns25,892 bytesremap_paths.pyruns34,904 bytesreporting.pyruns44,383 bytesreproducibility/compatibility_policy.jsonasset657 bytesreproducibility/pinned_versions.jsonasset2,649 bytessamplesheet_builder.pyruns43,827 bytesschemas.pyruns7,583 bytestests/conftest.pyruns4,134 bytestests/preflight_fixtures.pyruns1,856 bytestests/test_catalog_consistency.pyruns1,608 bytestests/test_cli_direct_invocation.pyruns1,598 bytestests/test_current_audit_regressions.pyruns1,640 bytestests/test_executor.pyruns6,357 bytestests/test_nfcore_sarek_wrapper.pyruns46,733 bytestests/test_outputs_parser.pyruns28,128 bytestests/test_params_builder.pyruns6,155 bytestests/test_portability_remap_interpreter.pyruns1,666 bytestests/test_preflight.pyruns50,063 bytestests/test_provenance.pyruns25,105 bytestests/test_remap_paths.pyruns12,708 bytestests/test_reporting.pyruns37,506 bytestests/test_samplesheet_builder.pyruns7,992 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubnfcore-scrnaseq-wrapper
When your agent uses it
Wrapper skill for running nf-core/scrnaseq 4.1.0 upstream single-cell RNA-seq preprocessing from FASTQ with strict preflight, reproducibility outputs, and downstream handoff to ClawBio scRNA skills.
What it loads into context
Frontmatter
533 tokensAlways available to the agent
SKILL.md
13,713 tokensWhen the skill is activated
Reference documents
7,529 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Scope
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- Algorithm / Methodology
- Presets
- nf-core/scrnaseq 4.1.0 Compatibility Policy
- Input & Reference Path Policy
- CLI Reference
- Output Structure
- Example Output
- Gotchas
- Safety
- Reproducibility Scope
- Agent Boundary
- Chaining Partners
- Maintenance
- Citations
Scripts executed separately
../../clawbio.py_isolated_imports.pycommand_builder.pyerrors.pyexecutor.pynfcore_4_1_0_contract.pynfcore_scrnaseq_wrapper.pyoutputs_parser.pyparams_builder.pypipeline_source.pypreflight.pyprovenance.pyremap_paths.pyreporting.pyrepro_commands.pysamplesheet_builder.pyschemas.pytests/conftest.pytests/test_audit_fixes.pytests/test_audit_round2.pytests/test_audit_round3.pytests/test_audit_round4.pytests/test_audit_round5.pytests/test_bundle_portability.pytests/test_cli_direct_invocation.pytests/test_command_builder.pytests/test_contract_generator.pytests/test_error_codes.pytests/test_executor.pytests/test_nfcore_contract.pytests/test_nfcore_scrnaseq_wrapper.pytests/test_outputs_parser.pytests/test_params_builder.pytests/test_pipeline_source.pytests/test_portability_remap_interpreter.pytests/test_preflight.pytests/test_provenance.pytests/test_remap_paths.pytests/test_reporting.pytests/test_repro_commands.pytests/test_resume_policy.pytests/test_samplesheet_builder.py
Files
../../clawbio.pyruns735 bytesCHANGELOG.mddoc24,274 bytesREADME.mddoc5,894 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytesSKILL.mdcore54,387 bytes_isolated_imports.pyruns1,266 bytescommand_builder.pyruns1,849 bytesdemo/README.mddoc320 byteserrors.pyruns3,415 bytesexecutor.pyruns10,312 bytesnfcore_4_1_0_contract.pyruns13,062 bytesnfcore_scrnaseq_wrapper.pyruns50,865 bytesoutputs_parser.pyruns16,735 bytesparams_builder.pyruns12,009 bytespipeline_source.pyruns7,165 bytespreflight.pyruns66,735 bytesprovenance.pyruns14,707 bytesremap_paths.pyruns27,874 bytesreporting.pyruns13,537 bytesrepro_commands.pyruns12,843 bytesreproducibility/compatibility_policy.jsonasset2,066 bytesreproducibility/pinned_versions.jsonasset775 bytessamplesheet_builder.pyruns32,704 bytesschemas.pyruns5,878 bytestests/conftest.pyruns4,134 bytestests/test_audit_fixes.pyruns25,290 bytestests/test_audit_round2.pyruns26,960 bytestests/test_audit_round3.pyruns17,642 bytestests/test_audit_round4.pyruns12,356 bytestests/test_audit_round5.pyruns15,841 bytestests/test_bundle_portability.pyruns10,680 bytestests/test_cli_direct_invocation.pyruns1,474 bytestests/test_command_builder.pyruns4,197 bytestests/test_contract_generator.pyruns2,824 bytestests/test_error_codes.pyruns2,520 bytestests/test_executor.pyruns11,062 bytestests/test_nfcore_contract.pyruns5,143 bytestests/test_nfcore_scrnaseq_wrapper.pyruns22,693 bytestests/test_outputs_parser.pyruns14,747 bytestests/test_params_builder.pyruns17,061 bytestests/test_pipeline_source.pyruns6,785 bytestests/test_portability_remap_interpreter.pyruns1,666 bytestests/test_preflight.pyruns29,758 bytestests/test_provenance.pyruns9,147 bytestests/test_remap_paths.pyruns23,095 bytestests/test_reporting.pyruns13,257 bytestests/test_repro_commands.pyruns4,028 bytestests/test_resume_policy.pyruns8,387 bytestests/test_samplesheet_builder.pyruns17,456 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubnutrigx
When your agent uses it
Personalised nutrition report from consumer genetic data (23andMe, AncestryDNA, VCF) — interrogates nutritionally-relevant SNPs and generates actionable dietary guidance, all computed locally.
What it loads into context
Frontmatter
278 tokensAlways available to the agent
SKILL.md
3,841 tokensWhen the skill is activated
Reference documents
2,866 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- What This Skill Does
- Trigger Phrases
- Curated SNP Panel
- Algorithm
- Usage
- File Structure
- Privacy
- Limitations & Disclaimer
- Roadmap
- References
- Contributing
Scripts executed separately
api.pyexamples/generate_patient.pyextract_genotypes.pygenerate_report.pynutrigx.pynutrigx_repro_bundle.pyparse_input.pypath_safety.pyscore_variants.pytests/test_ancestry_parser.pytests/test_genotype_validation.pytests/test_nutrigx.pytests/test_palindromic_snps.pytests/test_repro_bundle.pytests/test_rs953413_direction.py
Files
.gitignoreasset138 bytesSKILL.mdcore15,003 bytesSKILL.mdcore15,003 bytesSKILL.mdcore15,003 bytesapi.pyruns4,344 bytesdata/snp_panel.jsonasset5,717 bytesexamples/data/.gitkeepasset0 bytesexamples/generate_patient.pyruns8,849 bytesexamples/output/nutrigx_heatmap.pngasset165,774 bytesexamples/output/nutrigx_radar.pngasset206,138 bytesexamples/output/nutrigx_report.mddoc8,802 bytesextract_genotypes.pyruns6,387 bytesgenerate_report.pyruns17,268 bytesnutrigx.pyruns6,327 bytesnutrigx_repro_bundle.pyruns4,127 bytesparse_input.pyruns7,408 bytespath_safety.pyruns3,595 bytesscore_variants.pyruns3,732 bytestests/synthetic_patient.csvasset1,287 bytestests/test_ancestry_parser.pyruns1,332 bytestests/test_genotype_validation.pyruns3,146 bytestests/test_nutrigx.pyruns7,998 bytestests/test_palindromic_snps.pyruns1,965 bytestests/test_repro_bundle.pyruns6,965 bytestests/test_rs953413_direction.pyruns2,108 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubomics-target-evidence-mapper
When your agent uses it
Aggregate public target-level evidence across omics and translational sources for research triage.
What it loads into context
Frontmatter
160 tokensAlways available to the agent
SKILL.md
635 tokensWhen the skill is activated
Reference documents
76 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Demo mode
Scripts executed separately
commands.shomics_target_evidence_mapper.pytests/test_omics_target_evidence_mapper.pytests/test_omics_unavailable.pytests/test_smoke.py
Files
SKILL.mdcore2,600 bytesSKILL.mdcore2,600 bytesSKILL.mdcore2,600 bytescommands.shruns236 bytesenvironment.ymlasset140 bytesexamples/demo_input.jsonasset99 bytesexamples/expected_output.mddoc348 bytesomics_target_evidence_mapper.pyruns15,373 bytestests/test_omics_target_evidence_mapper.pyruns2,162 bytestests/test_omics_unavailable.pyruns6,783 bytestests/test_smoke.pyruns586 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHuborgan-aging-studio
When your agent uses it
Interactive Goeminne proteomic aging clock with organ filters and per-protein contribution breakdown (protein NPX × coefficient). Agent- and demo-friendly.
What it loads into context
Frontmatter
476 tokensAlways available to the agent
SKILL.md
2,309 tokensWhen the skill is activated
Reference documents
697 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Workflow
- Input Formats
- CLI Reference
- Demo
- Output Structure
- Gotchas
- Real-world data (download separately)
- Agent Boundary
- Safety
- Tests
- Citation
Scripts executed separately
organ_aging_studio.pytests/test_organ_aging_studio.py
Files
SKILL.mdcore8,885 bytesSKILL.mdcore8,885 bytesSKILL.mdcore8,885 bytesSKILL.mdcore8,885 bytesSKILL.mdcore8,885 bytesSKILL.mdcore8,885 bytesdata/PROVENANCE.mddoc2,517 bytesorgan_aging_studio.pyruns11,999 bytesrequirements.txtdoc39 bytestests/test_organ_aging_studio.pyruns4,361 bytes../proteomics-clock/data/demo_olink_npx.csv.gzasset1,639 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubpathway-enricher
When your agent uses it
Gene-set pathway enrichment analysis using Enrichr — queries KEGG, GO (BP/MF/CC), Reactome, WikiPathways, MSigDB, and Disease Ontology. Produces ranked pathway tables, interactive bubble charts, and a reproducible Markdown report.
What it loads into context
Frontmatter
181 tokensAlways available to the agent
SKILL.md
1,886 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Trigger
- Scope
- Input Formats
- Databases Queried
- Workflow
- Example Queries
- Output Structure
- Example Output
- Dependencies
- Safety
- Gotchas
- Agent Boundary
- Integration with Bio Orchestrator
Scripts executed separately
pathway_enricher.pytests/test_pathway_enricher.py
Files
SKILL.mdcore7,409 bytesSKILL.mdcore7,409 bytesSKILL.mdcore7,409 bytesdemo_genes.txtdoc301 bytespathway_enricher.pyruns26,380 bytestests/test_pathway_enricher.pyruns10,444 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubpharmgx-reporter
When your agent uses it
Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) — 12 genes, 31 SNPs, 51 drugs
What it loads into context
Frontmatter
194 tokensAlways available to the agent
SKILL.md
1,678 tokensWhen the skill is activated
Reference documents
5,771 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Genes Covered
- Drug Classes
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyapi.pypharmgx_reporter.pytests/test_pharmgx.py
Files
../../clawbio.pyruns735 bytesINTENTS.jsonasset686 bytesSKILL.mdcore6,355 bytesSKILL.mdcore6,355 bytesSKILL.mdcore6,355 bytesSKILL.mdcore6,355 bytesSKILL.mdcore6,355 bytesapi.pyruns3,544 bytesdemo_patient.txtdoc2,482 bytesdemo_report/report.mddoc12,318 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/criteria.jsonasset2,574 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/inputs/patient_data.txtdoc2,482 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/scenario.jsonasset92 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/task.mddoc1,475 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/criteria.jsonasset2,441 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/inputs/ancestry_patient.txtdoc919 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/scenario.jsonasset96 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-2/task.mddoc1,413 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-3/criteria.jsonasset2,497 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-3/inputs/partial_patient.txtdoc578 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-3/scenario.jsonasset97 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-3/task.mddoc1,297 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-4/criteria.jsonasset2,247 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-4/inputs/patient_warfarin.txtdoc656 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-4/scenario.jsonasset99 bytesevals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-4/task.mddoc1,423 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-0/criteria.jsonasset2,410 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-0/inputs/patient_data.txtdoc929 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-0/scenario.jsonasset75 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-0/task.mddoc1,415 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-2/criteria.jsonasset2,153 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-2/inputs/patient_data.txtdoc929 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-2/scenario.jsonasset81 bytesevals/019e830c-18c3-72cf-ab59-fc18afd404be/scenario-2/task.mddoc1,189 bytesexamples/demo_report.htmlasset59,859 bytespharmgx_reporter.pyruns99,535 bytestests/test_pharmgx.pyruns45,967 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubphylogenetics-builder
When your agent uses it
End-to-end ML phylogenetic tree inference — MSA, trimming, ModelFinder, IQ-TREE2/RAxML-NG.
What it loads into context
Frontmatter
642 tokensAlways available to the agent
SKILL.md
5,009 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Trigger
- Scope
- Workflow
- CLI Reference
- MSA Algorithm Guide
- Bootstrap Guide
- Example Output
- Output Structure
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Chaining Partners
- Dependencies
- Maintenance
- Citations
Scripts executed separately
api.pyphylogenetics_builder.pytests/test_phylogenetics_builder.py
Files
INTENTS.jsonasset670 bytesSKILL.mdcore17,985 bytesSKILL.mdcore17,985 bytesSKILL.mdcore17,985 bytesSKILL.mdcore17,985 bytesSKILL.mdcore17,985 bytesSKILL.mdcore17,985 bytesSKILL.mdcore17,985 bytesapi.pyruns951 bytesdemo_alignment.fastaasset6,303 bytesexamples/demo_tree.nwkasset359 bytesphylogenetics_builder.pyruns42,858 bytestests/test_phylogenetics_builder.pyruns35,281 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubpolars-bio
When your agent uses it
Fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames via polars-bio. A scalable bioframe/bedtools alternative.
What it loads into context
Frontmatter
728 tokensAlways available to the agent
SKILL.md
3,754 tokensWhen the skill is activated
Reference documents
3,755 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Polars & the Python ecosystem
- Input Formats
- Workflow
- CLI Reference
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Citation
Scripts executed separately
examples/generate_fixtures.pypolars_bio_runner.pytests/test_polars_bio.py
Files
SKILL.mdcore13,554 bytesSKILL.mdcore13,554 bytesSKILL.mdcore13,554 bytesexamples/demo.bamasset220 bytesexamples/demo.bam.baiasset176 bytesexamples/demo.bbasset804 bytesexamples/demo.bwasset724 bytesexamples/demo.fastaasset199 bytesexamples/demo.fastqasset153 bytesexamples/demo.gff3asset282 bytesexamples/demo.gtfasset346 bytesexamples/demo.pairsasset149 bytesexamples/demo.samasset410 bytesexamples/demo.vcfasset353 bytesexamples/demo_a.bedasset86 bytesexamples/demo_b.bedasset70 bytesexamples/generate_fixtures.pyruns2,699 bytespolars_bio_runner.pyruns18,686 bytesreferences/configuration.mddoc2,249 bytesreferences/file_io.mddoc3,011 bytesreferences/interval_operations.mddoc2,316 bytesreferences/pileup_operations.mddoc1,312 bytesreferences/polars_primer.mddoc3,451 bytesreferences/sql_processing.mddoc1,717 bytestests/test_polars_bio.pyruns17,297 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubpride-fetch
When your agent uses it
Query metadata and download data from the PRIDE Archive, EMBL-EBI's proteomics identifications database, via the PRIDE Archive REST API v3. Works with PRIDE/ProteomeXchange accessions (PXD, PRD) to fetch project metadata, list and download files (RAW, mzIdentML, mzML, mzTab, MGF, SDRF), search projects, emit a standardised metadata.tsv, write a quantms-ready minimal SDRF sample sheet, and generate a bash + SLURM download script.
What it loads into context
Frontmatter
739 tokensAlways available to the agent
SKILL.md
4,302 tokensWhen the skill is activated
Reference documents
5,233 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pypride_fetch.pypride_fetch_api.pytests/test_pride_fetch.py
Files
../../clawbio.pyruns735 bytes../../docs/data-handling.mddoc19,645 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesSKILL.mdcore17,059 bytesexamples/demo_PXD084218_files.jsonasset25,187 bytesexamples/demo_PXD084218_project.jsonasset8,325 bytesexamples/demo_PXD084218_sdrf_links.jsonasset3 bytesexamples/demo_search.jsonasset8,999 bytespride_fetch.pyruns8,850 bytespride_fetch_api.pyruns32,754 bytestests/test_pride_fetch.pyruns17,313 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubprofile-report
When your agent uses it
Unified personal genomic profile report — reads a PatientProfile JSON and synthesizes all skill results into a single "Your Genomic Profile" document.
What it loads into context
Frontmatter
379 tokensAlways available to the agent
SKILL.md
1,958 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- PRS evidence scope
Scripts executed separately
../../clawbio.pyprofile_report.pytests/__init__.pytests/test_profile_report.pytests/test_profile_reproducibility.py
Files
../../clawbio.pyruns735 bytesINTENTS.jsonasset679 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesSKILL.mdcore8,530 bytesdemo_full_profile.jsonasset40,361 bytesprofile_report.pyruns37,582 bytestests/__init__.pyruns0 bytestests/fixtures/mock_profile.jsonasset4,688 bytestests/test_profile_report.pyruns14,550 bytestests/test_profile_reproducibility.pyruns6,761 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubproteomics-clock
When your agent uses it
Compute organ-specific biological age from Olink proteomic data using Goeminne et al. (2025) elastic net aging clocks.
What it loads into context
Frontmatter
469 tokensAlways available to the agent
SKILL.md
3,052 tokensWhen the skill is activated
Reference documents
176 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Output
- Output Structure
- Gotchas
- Network Calls
- Safety
- Agent Boundary
- Longitudinal / Treatment Effect Analysis
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
examples/fetch_filbin.pyexamples/treatment_effect_covid.pyproteomics_clock.pytests/test_proteomics_clock.py
Files
SKILL.mdcore11,778 bytesSKILL.mdcore11,778 bytesSKILL.mdcore11,778 bytesSKILL.mdcore11,778 bytesSKILL.mdcore11,778 bytesdata/PROVENANCE.mddoc555 bytesdata/demo_olink_npx.csv.gzasset1,639 bytesexamples/fetch_filbin.pyruns5,758 bytesexamples/treatment_effect_covid.pyruns10,153 bytesproteomics_clock.pyruns24,905 bytesrequirements.txtdoc14 bytestests/test_proteomics_clock.pyruns6,602 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubproteomics-de
When your agent uses it
Differential expression analysis for label-free quantitative (LFQ) intensity data with standard MaxQuant and DIA-NN output. Workflow includes preprocessing, imputation, and statistical testing.
What it loads into context
Frontmatter
215 tokensAlways available to the agent
SKILL.md
1,716 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Domain Decisions
- Safety Rules
- Agent Boundary
- Input Contract
- Output Structure
- Usage
- References
Scripts executed separately
proteomics_de.pytests/test_proteomics_de.py
Files
SKILL.mdcore6,641 bytesSKILL.mdcore6,641 bytesSKILL.mdcore6,641 bytesSKILL.mdcore6,641 bytesSKILL.mdcore6,641 bytesSKILL.mdcore6,641 bytesexamples/test_diann.tsvasset1,450 bytesexamples/test_metadata.csvasset220 bytesexamples/test_metadata_diann.csvasset298 bytesexamples/test_proteinGroups.txtdoc869,468 bytesproteomics_de.pyruns27,293 bytestests/test_proteomics_de.pyruns9,248 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubprotocols-io
When your agent uses it
Search, browse, and retrieve scientific protocols from protocols.io via REST API. Client token authentication for private protocols. Use when user mentions protocols.io, lab protocols, DOI lookup, protocol search, protocol steps, or scientific methods.
What it loads into context
Frontmatter
216 tokensAlways available to the agent
SKILL.md
1,866 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Authentication
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyprotocols_io.pytests/test_protocols_io.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore7,572 bytesSKILL.mdcore7,572 bytesSKILL.mdcore7,572 bytesSKILL.mdcore7,572 bytesdemo/demo_protocol.jsonasset2,911 bytesdemo/demo_search_results.jsonasset2,173 bytesprotocols_io.pyruns26,605 bytestests/test_protocols_io.pyruns28,257 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubprs-abstain
When your agent uses it
Gates polygenic risk score percentiles on trait applicability, score integrity and ancestry transferability, withholding the percentile when it would be uninterpretable and attributing the error to individual SNPs.
What it loads into context
Frontmatter
768 tokensAlways available to the agent
SKILL.md
6,210 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Domain Decisions
- Safety Rules
- Agent Boundary
- Chaining Partners
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
pdf_report.pyprs_abstain.pytests/test_prs_abstain.py
Files
SKILL.mdcore25,835 bytesSKILL.mdcore25,835 bytesSKILL.mdcore25,835 bytesSKILL.mdcore25,835 bytesSKILL.mdcore25,835 bytesSKILL.mdcore25,835 bytesSKILL.mdcore25,835 bytesSKILL.mdcore25,835 bytesexamples/demo_genotype.txtdoc10,482 bytesexamples/demo_population_af.tsvasset8,307 bytesexamples/demo_prs_results.jsonasset7,949 bytesexamples/demo_query_individuals.csvasset211 bytesexamples/demo_reference_pcs.csvasset2,598 bytesexamples/scores/CLAWBIO-AF-12_GRCh37.txtdoc1,477 bytesexamples/scores/CLAWBIO-BC-77_GRCh37.txtdoc3,898 bytesexamples/scores/CLAWBIO-BMI-97_GRCh37.txtdoc4,494 bytesexamples/scores/CLAWBIO-CAD-46_GRCh37.txtdoc2,711 bytesexamples/scores/CLAWBIO-PC-147_GRCh37.txtdoc6,340 bytesexamples/scores/CLAWBIO-T2D-8_GRCh37.txtdoc1,325 bytespdf_report.pyruns9,623 bytesprs_abstain.pyruns128,438 bytestests/fixtures/PGS000001_hmPOS_GRCh37_authentic.txtdoc7,003 bytestests/fixtures/single_individual_eur.csvasset120 bytestests/test_prs_abstain.pyruns115,101 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubprs-applicability-gate
When your agent uses it
Deterministic gate for ONE already-computed polygenic score result and ONE person: returns SUPPORTED (raw score, standardised score and reference percentile may be shown), RAW_ONLY (raw score only) or ABSTAIN (nothing), with reason codes, a full rule trace and what would change the result. Never produces absolute risk.
What it loads into context
Frontmatter
580 tokensAlways available to the agent
SKILL.md
6,264 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyprs_applicability_gate.pytests/test_prs_applicability_gate.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore24,824 bytesSKILL.mdcore24,824 bytesSKILL.mdcore24,824 bytesSKILL.mdcore24,824 bytesSKILL.mdcore24,824 bytesSKILL.mdcore24,824 bytesconfig/calibration.yamlasset2,882 bytesexamples/synthetic_A_supported.gate_input.jsonasset3,867 bytesexamples/synthetic_B_raw_only.gate_input.jsonasset3,897 bytesexamples/synthetic_C_abstain.gate_input.jsonasset3,830 bytesprs_applicability_gate.pyruns45,724 bytestests/test_prs_applicability_gate.pyruns47,974 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubpubmed-summariser
When your agent uses it
Search PubMed, preserve complete abstracts and sections, and produce research briefings with abstract openings or optional OpenAI/Ollama summaries.
What it loads into context
Frontmatter
299 tokensAlways available to the agent
SKILL.md
2,970 tokensWhen the skill is activated
Reference documents
850 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Trigger
- Scope
- Input Formats
- Workflow
- Algorithm / Methodology
- Output Structure
- Example Output
- Dependencies
- Gotchas
- Safety
- Integration with Bio Orchestrator
- Agent Boundary
- Chaining Partners
- Maintenance
Scripts executed separately
../../clawbio.pyabstract_summary.pyexamples/run_briefing.pypubmed_api.pypubmed_summariser.pytests/__init__.pytests/test_pubmed_api.pytests/test_pubmed_summariser.pytests/test_workflow.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesSKILL.mdcore13,313 bytesabstract_summary.pyruns3,389 bytesexamples/.env.exampleasset420 bytesexamples/README.mddoc3,530 bytesexamples/run_briefing.pyruns3,001 bytespubmed_api.pyruns7,217 bytespubmed_summariser.pyruns16,322 bytestests/__init__.pyruns0 bytestests/fixtures/sample_papers.jsonasset631 bytestests/test_pubmed_api.pyruns8,258 bytestests/test_pubmed_summariser.pyruns4,850 bytestests/test_workflow.pyruns11,678 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubrare-disease-rnaseq
When your agent uses it
Blood RNA-seq expression-outlier detection for rare-disease diagnostics. Cases scored against a control reference panel; outliers ranked and filtered by a haploinsufficient disease-gene panel.
What it loads into context
Frontmatter
292 tokensAlways available to the agent
SKILL.md
1,237 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- When To Use
- Method
- Input Contract
- Output Structure
- Demo
- Production Path (Sidra / QBB Reference)
- Safety
- Disclaimer
Scripts executed separately
rare_disease_rnaseq.pytests/test_rare_disease_rnaseq.py
Files
SKILL.mdcore5,007 bytesSKILL.mdcore5,007 bytesSKILL.mdcore5,007 bytesSKILL.mdcore5,007 bytesdata/disease_panel.csvasset2,546 bytesrare_disease_rnaseq.pyruns14,441 bytestests/test_rare_disease_rnaseq.pyruns4,304 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubrare-high-impact-variants
When your agent uses it
Count rare, high-impact loss-of-function variants carried in a VCF, annotated with molecular consequence and population allele frequency
What it loads into context
Frontmatter
340 tokensAlways available to the agent
SKILL.md
2,470 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyapi.pyrare_high_impact_variants.pytests/test_logic.pytests/test_rare_high_impact_variants.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore10,260 bytesSKILL.mdcore10,260 bytesSKILL.mdcore10,260 bytesSKILL.mdcore10,260 bytesSKILL.mdcore10,260 bytesSKILL.mdcore10,260 bytesapi.pyruns671 bytesbench_test_cases/rhi_01_basic_correct/ground_truth.txtdoc602 bytesbench_test_cases/rhi_01_basic_correct/input.txtdoc334 bytesbench_test_cases/rhi_02_empty_input/ground_truth.txtdoc369 bytesbench_test_cases/rhi_02_empty_input/input.txtdoc74 bytesbench_test_cases/rhi_03_malformed_input/ground_truth.txtdoc452 bytesbench_test_cases/rhi_03_malformed_input/input.txtdoc92 bytesdemo_input.txtdoc1,676 bytesrare_high_impact_variants.pyruns13,102 bytestests/test_logic.pyruns3,742 bytestests/test_rare_high_impact_variants.pyruns7,243 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubrecombinator
When your agent uses it
Produce offspring genomes from parent pairs via meiotic recombination, mutation, and clinical evaluation
What it loads into context
Frontmatter
175 tokensAlways available to the agent
SKILL.md
700 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Purpose
- How It Works
- Input
- Output
- CLI Usage
- Output Format
Scripts executed separately
recombinator.py
Files
SKILL.mdcore2,607 bytesSKILL.mdcore2,607 bytesSKILL.mdcore2,607 bytesrecombinator.pyruns4,954 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubrepro-enforcer
When your agent uses it
Export any bioinformatics analysis as a reproducible bundle with Conda environment, Singularity container definition, and Nextflow pipeline.
What it loads into context
Frontmatter
121 tokensAlways available to the agent
SKILL.md
400 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Dependencies
- Example Queries
- Status
Files
SKILL.mdcore1,656 bytesSKILL.mdcore1,656 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubrnaseq-de
When your agent uses it
Differential expression analysis for bulk RNA-seq and pseudo-bulk count matrices with QC, PCA, and contrast testing.
What it loads into context
Frontmatter
259 tokensAlways available to the agent
SKILL.md
637 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Input Contract
- Output Structure
- Usage
- Safety
Scripts executed separately
rnaseq_de.pytests/test_rnaseq_de.py
Files
SKILL.mdcore2,360 bytesSKILL.mdcore2,360 bytesSKILL.mdcore2,360 bytesSKILL.mdcore2,360 bytesexamples/demo_counts.csvasset309 bytesexamples/demo_metadata.csvasset130 bytesrnaseq_de.pyruns27,245 bytestests/fixtures/pseudobulk_counts.csvasset391 bytestests/fixtures/pseudobulk_metadata.csvasset279 bytestests/test_rnaseq_de.pyruns17,105 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubsample-qc-triage
When your agent uses it
Deterministic multi-sample QC triage for identity, sex, contamination, and batch-shift outliers
What it loads into context
Frontmatter
342 tokensAlways available to the agent
SKILL.md
1,636 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Chaining Partners
- Maintenance
- Author & Attribution
- Citations
Scripts executed separately
../../clawbio.pysample_qc_triage.pytests/test_sample_qc_triage.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesSKILL.mdcore6,872 bytesdemo_qc_metrics.csvasset421 bytessample_qc_triage.pyruns9,616 bytestests/test_sample_qc_triage.pyruns6,319 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubscrna-embedding
When your agent uses it
Local scVI/scANVI-based single-cell latent embedding and batch-aware integration from raw-count .h5ad or 10x Matrix Market input, with stable integrated AnnData export for downstream latent analysis.
What it loads into context
Frontmatter
278 tokensAlways available to the agent
SKILL.md
2,150 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyscrna_embedding.pytests/test_scrna_embedding.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore8,137 bytesSKILL.mdcore8,137 bytesSKILL.mdcore8,137 bytesSKILL.mdcore8,137 bytesSKILL.mdcore8,137 bytesscrna_embedding.pyruns40,066 bytestests/test_scrna_embedding.pyruns20,555 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubscrna-orchestrator
When your agent uses it
Local Scanpy pipeline for single-cell RNA-seq QC, optional doublet detection, clustering, marker discovery, optional CellTypist annotation, optional latent downstream mode from integrated.h5ad/X_scvi, and optional dataset-level plus within-cluster contrastive marker analysis from raw-count .h5ad or 10x Matrix Market input.
What it loads into context
Frontmatter
336 tokensAlways available to the agent
SKILL.md
2,988 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Status
- Citations
Scripts executed separately
../../clawbio.pyscrna_orchestrator.pytests/test_scrna_orchestrator.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore11,633 bytesSKILL.mdcore11,633 bytesSKILL.mdcore11,633 bytesSKILL.mdcore11,633 bytesSKILL.mdcore11,633 bytesscrna_orchestrator.pyruns61,886 bytestests/test_scrna_orchestrator.pyruns41,072 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubseq-wrangler
When your agent uses it
NGS read QC, alignment, and BAM processing pipeline. Wraps FastQC, BWA/Bowtie2/Minimap2, SAMtools, and MultiQC for automated read-to-BAM workflows.
What it loads into context
Frontmatter
586 tokensAlways available to the agent
SKILL.md
2,792 tokensWhen the skill is activated
Reference documents
1,625 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Output Structure
- Dependencies
- Gotchas
- Agent Boundary
- Safety
- Integration with Bio Orchestrator
- Example Queries
- Citations
Scripts executed separately
seq_wrangler.pytests/test_seq_wrangler.py
Files
README.mddoc3,307 bytesSKILL.mdcore10,123 bytesSKILL.mdcore10,123 bytesSKILL.mdcore10,123 bytesSKILL.mdcore10,123 bytesSKILL.mdcore10,123 bytesSKILL.mdcore10,123 bytesexamples/demo-results/report.mddoc2,082 bytesseq_wrangler.pyruns30,416 bytestests/test_seq_wrangler.pyruns3,201 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubskill-builder
When your agent uses it
Scaffold a new ClawBio skill from a spec file (JSON/YAML) or interactively — generates SKILL.md, Python skeleton, tests, and updates catalog.json
What it loads into context
Frontmatter
204 tokensAlways available to the agent
SKILL.md
2,114 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Spec File Reference
- Algorithm / Methodology
- Example Queries
- Output Structure
- Dependencies
- Safety
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pyskill_builder.pytests/test_skill_builder.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore8,460 bytesSKILL.mdcore8,460 bytesSKILL.mdcore8,460 bytesSKILL.mdcore8,460 bytesSKILL.mdcore8,460 bytesdemo_spec.jsonasset1,207 bytesskill_builder.pyruns77,092 bytestemplates/spec_template.jsonasset3,100 bytestests/test_skill_builder.pyruns48,472 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubspatial-transcriptomics
When your agent uses it
Analyse 10x Visium spatial transcriptomics: SpaceRanger outs or spatial h5ad in, then QC, Leiden clustering, Wilcoxon markers, Moran's I, neighbourhood enrichment and co-occurrence in one local report.
What it loads into context
Frontmatter
496 tokensAlways available to the agent
SKILL.md
4,540 tokensWhen the skill is activated
Reference documents
1,348 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Validation and Replay
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pyfixtures/generate_squidpy_v1_6_fixture.pyspatial_report.pyspatial_stats.pyspatial_transcriptomics.pytests/test_spatial_regressions.pytests/test_spatial_report.pytests/test_spatial_stats.pytests/test_spatial_transcriptomics.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesSKILL.mdcore17,454 bytesexamples/demo_spec.jsonasset363 bytesexamples/public_visium_validation.mddoc5,192 bytesfixtures/generate_squidpy_v1_6_fixture.pyruns3,637 bytesfixtures/squidpy_v1_6_co_occurrence.jsonasset1,796 bytesspatial_report.pyruns17,473 bytesspatial_stats.pyruns11,783 bytesspatial_transcriptomics.pyruns36,244 bytestests/test_spatial_regressions.pyruns11,445 bytestests/test_spatial_report.pyruns6,086 bytestests/test_spatial_stats.pyruns4,233 bytestests/test_spatial_transcriptomics.pyruns10,332 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubstruct-predictor
When your agent uses it
Protein structure prediction with Boltz-2 (default) or OpenFold3. Accepts YAML inputs (single protein or multi-chain complex), runs the chosen backend offline, extracts per-residue pLDDT and PAE confidence, and writes a markdown report with figures.
What it loads into context
Frontmatter
278 tokensAlways available to the agent
SKILL.md
2,013 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- CLI Reference
- Output Structure
- YAML Complex Format
- pLDDT Confidence Bands
- Demo Data
- Gotchas
- Dependencies
- Citations
Scripts executed separately
struct_predictor.pystruct_predictor_core/__init__.pystruct_predictor_core/confidence.pystruct_predictor_core/io.pystruct_predictor_core/predict.pystruct_predictor_core/report.pystruct_predictor_core/viewer.pytests/__init__.pytests/test_struct_predictor.py
Files
SKILL.mdcore7,411 bytesSKILL.mdcore7,411 bytesSKILL.mdcore7,411 bytesSKILL.mdcore7,411 bytesSKILL.mdcore7,411 bytesdemo_data/trpcage.yamlasset101 bytesstruct_predictor.pyruns7,445 bytesstruct_predictor_core/__init__.pyruns0 bytesstruct_predictor_core/confidence.pyruns6,416 bytesstruct_predictor_core/io.pyruns8,210 bytesstruct_predictor_core/predict.pyruns5,847 bytesstruct_predictor_core/report.pyruns9,985 bytesstruct_predictor_core/viewer.pyruns8,484 bytestests/__init__.pyruns0 bytestests/test_struct_predictor.pyruns34,012 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubtarget-validation-scorer
When your agent uses it
Evidence-grounded target validation scoring with GO/NO-GO decisions for drug discovery campaigns
What it loads into context
Frontmatter
417 tokensAlways available to the agent
SKILL.md
2,095 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Example Queries
- Output Structure
- Workflow
- Domain Decisions
- Safety Rules
- Agent Boundary
Scripts executed separately
commands.shtarget_validation_scorer.pytests/test_target_validation_scorer.py
Files
SKILL.mdcore9,256 bytesSKILL.mdcore9,256 byteschecksums.sha256asset411 bytescommands.shruns357 bytesdemo_input.jsonasset2,947 bytesenvironment.ymlasset154 bytestarget_validation_scorer.pyruns14,935 bytestests/test_target_validation_scorer.pyruns10,661 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubturingdb-graph
When your agent uses it
Build, query, and analyse biomedical knowledge graphs in TuringDB, a columnar graph database with git-like versioning.
What it loads into context
Frontmatter
727 tokensAlways available to the agent
SKILL.md
4,346 tokensWhen the skill is activated
Reference documents
12,890 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Example Queries
- Example Output
- Output Structure
- Algorithm / Methodology
- Dependencies
- Gotchas
- Safety
- Domain Decisions
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
http_server.pytests/test_turingdb_graph.pyturingdb_graph.py
Files
SKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesSKILL.mdcore16,963 bytesdemo/antibody.csvasset1,412 bytesdemo/cohort.csvasset1,540 bytesdemo/pathway.gmlasset4,118 byteshttp_server.pyruns3,738 bytesreference/algorithms.mddoc5,212 bytesreference/biomedical.mddoc19,798 bytesreference/introspection.mddoc3,717 bytesreference/querying.mddoc5,602 bytesreference/startup.mddoc4,450 bytesreference/writing.mddoc10,011 bytesrequirements.txtdoc134 bytestests/test_turingdb_graph.pyruns4,828 bytesturingdb_graph.pyruns28,472 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubukb-navigator
When your agent uses it
Semantic search across UK Biobank's 12,000+ data fields and publications — find the right variables for your research question.
What it loads into context
Frontmatter
135 tokensAlways available to the agent
SKILL.md
986 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Core Capabilities
- Input Formats
- Data Sources
- Workflow
- Example Queries
- Output Structure
- Demo Mode
- Dependencies
- Safety
- Integration with Bio Orchestrator
Scripts executed separately
tests/test_ukb_navigator.pyukb_navigator.py
Files
SKILL.mdcore4,105 bytesSKILL.mdcore4,105 bytesSKILL.mdcore4,105 bytesSKILL.mdcore4,105 bytestests/test_ukb_navigator.pyruns6,859 bytesukb_navigator.pyruns15,912 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubukb-ppp-region-fetch
When your agent uses it
Fetch a regional slice of plasma pQTL summary statistics from the UK Biobank Pharma Proteomics Project (UKB-PPP; Sun 2023 Nature) for a specific (protein, ancestry) measurement. Use when an agent needs per-variant beta / SE / p-value around a coloc-lead variant for downstream colocalisation, Mendelian randomisation, or regional plotting against a pQTL exposure. The canonical use case is the cis-window around the protein's coding gene TSS, but UKB-PPP releases full-genome summary stats per protein so any GRCh38 window (including trans loci) is supported when the user supplies an explicit (chromosome, start_bp, end_bp). Input: protein_label (HGNC or UniProt), ancestry, chromosome, start_bp, end_bp. Output: harmonised TSV slice + manifest + human-readable report.
What it loads into context
Frontmatter
1,129 tokensAlways available to the agent
SKILL.md
5,183 tokensWhen the skill is activated
Reference documents
2,064 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- First-time setup (IMPORTANT)
- Overview
- Trigger
- Scope
- Workflow
- CLI Reference
- Example Output
- Gotchas
- Safety
- Agent Boundary
- Citations
Scripts executed separately
../../clawbio.pytests/conftest.pytests/test_live_ukb_ppp_region_fetch.pytests/test_ukb_ppp_region_fetch.pyukb_ppp_region_fetch.py
Files
../../clawbio.pyruns735 bytes.gitignoreasset259 bytesLICENSEasset1,067 bytesSKILL.mdcore19,821 bytesSKILL.mdcore19,821 bytesSKILL.mdcore19,821 bytesSKILL.mdcore19,821 bytesSKILL.mdcore19,821 bytesbundled_slices/README.mddoc3,588 bytesbundled_slices/SORT1__EUR__chr1__108774968_109774968.json.gzasset425,957 bytesenvironment.ymlasset212 bytesexamples/default.jsonasset488 bytesexamples/expected_output.mddoc3,190 bytesexamples/sort1_ukb_ppp_eur.jsonasset488 bytestests/conftest.pyruns662 bytestests/test_live_ukb_ppp_region_fetch.pyruns2,868 bytestests/test_ukb_ppp_region_fetch.pyruns28,564 bytesukb_ppp_region_fetch.pyruns46,724 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubvariant-annotation
When your agent uses it
Annotate VCF variants with Ensembl VEP REST, ClinVar significance, gnomAD/population frequency context, and prioritized variant ranking.
What it loads into context
Frontmatter
422 tokensAlways available to the agent
SKILL.md
2,560 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Why This Exists
- Core Capabilities
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Domain Decisions
- Example Queries
- Output Structure
- Dependencies
- Safety
- Safety Rules
- Agent Boundary
- Integration with Bio Orchestrator
- Citations
Scripts executed separately
../../clawbio.pytests/test_variant_annotation.pyvariant_annotation.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore11,141 bytesSKILL.mdcore11,141 bytesSKILL.mdcore11,141 bytesSKILL.mdcore11,141 bytesSKILL.mdcore11,141 bytesexample_data/synthetic_clinvar_panel.vcfasset2,591 bytesfigures/variant_annotation_summary.pngasset128,742 bytesrequirements.txtdoc72 bytestests/test_variant_annotation.pyruns16,009 bytesvariant_annotation.pyruns55,572 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubvcf-annotator
When your agent uses it
Annotate VCF variants with Ensembl VEP, ClinVar, and gnomAD. Ranks variants by impact (HIGH/MODERATE/LOW/MODIFIER) and generates a reproducible report.
What it loads into context
Frontmatter
415 tokensAlways available to the agent
SKILL.md
2,825 tokensWhen the skill is activated
Reference documents
1,236 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Citations
Scripts executed separately
../../clawbio.pytests/test_vcf_annotator.pyvcf_annotator.py
Files
../../clawbio.pyruns735 bytesSKILL.mdcore10,487 bytesSKILL.mdcore10,487 bytesSKILL.mdcore10,487 bytesSKILL.mdcore10,487 bytesexamples/demo_output/report.mddoc3,502 bytestests/test_vcf_annotator.pyruns20,367 bytesvcf_annotator.pyruns22,085 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubwes-clinical-report-en
When your agent uses it
Generates professional clinical PDF reports in English from WES (Whole Exome Sequencing) data with clinical interpretation summary, pharmacogenomic alerts, and follow-up recommendations.
What it loads into context
Frontmatter
373 tokensAlways available to the agent
SKILL.md
1,849 tokensWhen the skill is activated
Reference documents
1,839 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Scope
- Workflow
- Capabilities
- Example Output
- Usage
- Input format
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Requirements
- Privacy
- References
Scripts executed separately
tests/test_wes_clinical_report_en.pywes_clinical_report_en.py
Files
SKILL.mdcore7,372 bytesSKILL.mdcore7,372 bytesSKILL.mdcore7,372 bytesexamples/demo_WES_Report.mddoc6,480 bytesrequirements.txtdoc15 bytestests/test_wes_clinical_report_en.pyruns15,655 byteswes_clinical_report_en.pyruns48,395 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubwes-clinical-report-es
When your agent uses it
Generates professional clinical PDF reports in Spanish from WES (Whole Exome Sequencing) data with clinical interpretation, pharmacogenomic alerts, and follow-up recommendations.
What it loads into context
Frontmatter
391 tokensAlways available to the agent
SKILL.md
2,123 tokensWhen the skill is activated
Reference documents
1,839 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Scope
- Workflow
- Capabilities
- Example Output
- Usage
- Input format
- Gotchas
- Safety
- Agent Boundary
- Chaining Partners
- Maintenance
- Requirements
- Privacy
- References
Scripts executed separately
tests/test_wes_clinical_report_es.pywes_clinical_report_es.py
Files
SKILL.mdcore8,429 bytesSKILL.mdcore8,429 bytesSKILL.mdcore8,429 bytesexamples/demo_WES_Report.mddoc6,480 bytesrequirements.txtdoc15 bytestests/test_wes_clinical_report_es.pyruns15,825 byteswes_clinical_report_es.pyruns65,548 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubwgs-prs
When your agent uses it
End-to-end WGS to polygenic risk score pipeline. Takes paired-end FASTQ files (or a pre-existing VCF) through nf-core/sarek for variant calling, applies VCF QC (normalisation, hard filtering, Ti/Tv and Het/Hom checks), then computes polygenic risk scores via the PGS Catalog. Fills the FASTQ to VCF gap upstream of the gwas-prs skill.
What it loads into context
Frontmatter
789 tokensAlways available to the agent
SKILL.md
3,569 tokensWhen the skill is activated
Reference documents
0 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Scope
- Pipeline Stages
- Entry Points
- Workflow
- Usage
- Key Design Decisions
- Example Output
- Output Structure
- Chaining with other ClawBio Skills
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
Scripts executed separately
tests/test_repro_bundle.pytests/test_sarek.pytests/test_vcf_qc.pytests/test_wgs_prs.pywgs_prs.pywgs_prs_repro_bundle.py
Files
SKILL.mdcore13,059 bytesSKILL.mdcore13,059 bytesSKILL.mdcore13,059 bytestests/test_repro_bundle.pyruns15,693 bytestests/test_sarek.pyruns6,304 bytestests/test_vcf_qc.pyruns11,887 bytestests/test_wgs_prs.pyruns12,926 byteswgs_prs.pyruns29,073 byteswgs_prs_repro_bundle.pyruns10,066 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubxena-tcga-gene-query
When your agent uses it
Query TCGA tumor biology through the ucscxenatoolspy API. Supports tumor-vs-normal differential expression, gene-gene correlation, survival association, and cancer catalogue browsing across 30+ TCGA cancer types.
What it loads into context
Frontmatter
588 tokensAlways available to the agent
SKILL.md
4,927 tokensWhen the skill is activated
Reference documents
2,043 tokensLoaded on request
Token counts are estimates. Scripts run separately; they are not counted as reference context.
The playbook
- Trigger
- Why This Exists
- Core Capabilities
- Scope
- Input Formats
- Workflow
- CLI Reference
- Demo
- Algorithm / Methodology
- Example Queries
- Example Output
- Output Structure
- Dependencies
- Gotchas
- Safety
- Agent Boundary
- Integration with Bio Orchestrator
- Maintenance
- Natural Language Cancer Mapping
- Citations
Scripts executed separately
scripts/query_tcga_api.pytests/test_query.py
Files
SKILL.mdcore19,276 bytesSKILL.mdcore19,276 bytesSKILL.mdcore19,276 bytesSKILL.mdcore19,276 bytesSKILL.mdcore19,276 bytesSKILL.mdcore19,276 bytesSKILL.mdcore19,276 bytesexamples/demo_output.mddoc2,288 bytesreferences/api.mddoc2,392 bytesreferences/tcga_codes.mddoc1,991 bytesscripts/query_tcga_api.pyruns24,350 bytestests/test_query.pyruns13,955 bytes
No excerpt is shown for this license. Read the source on GitHub.
View the complete source on GitHubSkills included
- affinity-proteomics
- analyze-fasta
- ancestry-risk-profiler
- archaic-introgression
- arrayexpress-fetch
- article-data-fetcher
- bgpt-mcp
- bigquery-public
- bio-orchestrator
- bioconductor-bridge
- bioqc-mcp
- biostudies-fetch
- busco-assessor
- cell-detection
- celltype-specificity-profiler
- claw-amplicon-qc
- claw-ancestry-pca
- claw-metagenomics
- claw-methylation-cycle
- claw-semantic-sim
- clawpathy-autoresearch
- clinical-trial-finder
- clinical-variant-prioritizer
- clinical-variant-reporter
- clinpgx
- cnv-acmg-classifier
- crispr-screen-triage
- data-extractor
- de-summary
- deepspot-m
- diff-visualizer
- dnasp
- drug-photo
- drug-repurposing-screen
- ena-fetch
- eqtl-catalogue-region-fetch
- equity-scorer
- fastreer
- fine-mapping
- flow-bio
- galaxy-bridge
- genome-compare
- genome-match
- geo-fetch
- gi-annotation
- gi-chromatin
- gi-enhancer
- gi-expression
- gi-promoter
- gi-splice
- gwas-catalog-region-fetch
- gwas-lookup
- gwas-pipeline
- gwas-prs
- gwas-sumstats-harmonize
- hla-typing
- igv-validator
- illumina-bridge
- just-prs-mcp
- labstep
- ld-1000g-region-compute
- lit-synthesizer
- locuscompare-region-render
- marker-dominance-mapper
- mendelian-randomisation
- methylation-clock
- multiqc-reporter
- ncbi-datasets
- nfcore-rnaseq-wrapper
- nfcore-rnastructurome-wrapper
- nfcore-sarek-wrapper
- nfcore-scrnaseq-wrapper
- nutrigx
- omics-target-evidence-mapper
- organ-aging-studio
- pathway-enricher
- pharmgx-reporter
- phylogenetics-builder
- polars-bio
- pride-fetch
- profile-report
- proteomics-clock
- proteomics-de
- protocols-io
- prs-abstain
- prs-applicability-gate
- pubmed-summariser
- rare-disease-rnaseq
- rare-high-impact-variants
- recombinator
- repro-enforcer
- rnaseq-de
- sample-qc-triage
- scrna-embedding
- scrna-orchestrator
- seq-wrangler
- skill-builder
- spatial-transcriptomics
- struct-predictor
- target-validation-scorer
- turingdb-graph
- ukb-navigator
- ukb-ppp-region-fetch
- variant-annotation
- vcf-annotator
- wes-clinical-report-en
- wes-clinical-report-es
- wgs-prs
- xena-tcga-gene-query
Repository facts
- License
- No license detected
- Created
- Feb 25, 2026
- Last pushed
- Nov 5, 2026
- Forks
- 295
- Open issues
- 24
- Project activity
- Active
Rank over the last 12 weeks
Now #784 · best #529 · down 153 in 30 days
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- #784 since Nov 5
57 earlier periods
- #516 on Aug 2
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- #532 from Aug 11 to Aug 14
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- #750 on Oct 25
- #760 on Oct 28
- #763 on Oct 29
- #767 on Oct 30
Before you install
Network or broad shellAutomated signals, not a guarantee
Checked Nov 3, 2026
Not fully analyzed: some files were too long, unreadable or missing. This never lowers the level.
Show 583 notes
commands/new-skill.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedcommands/new-skill.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedcommands/new-skill.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedcommands/new-skill.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedcommands/new-skill.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedcommands/run-demo.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/affinity-proteomics/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/affinity-proteomics/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/affinity-proteomics/SKILL.md:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/catalog.json:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/dnasp/environment.yml:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/eqtl-catalogue-region-fetch/data/dataset_index_r7.provenance.json:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/eqtl-catalogue-region-fetch/data/dataset_index_r7.provenance.json:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/eqtl-catalogue-region-fetch/data/dataset_index_r7.provenance.json:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/eqtl-catalogue-region-fetch/data/dataset_index_r7.provenance.json:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/galaxy-bridge/galaxy_catalog.json:1Analysis incomplete: file exceeds text byte budgetskills/galaxy-bridge/galaxy_catalog.json:10102Analysis incomplete: regex work limit reachedskills/galaxy-bridge/galaxy_catalog.json:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/galaxy-bridge/galaxy_catalog.json:1Analysis incomplete: Referenced executable target unavailable; not analyzedskills/gwas-lookup/tests/fixtures/gwas_catalog_v2_rs7903146_page0.json:10265Analysis incomplete: regex work limit reached
- 2 broad permissionsin 1 file: skills/dnasp/SKILL.md:1
- 58 dangerous shell commandsin 18 files: skills/dnasp/dnasp.py:33 skills/dnasp/tests/test_dnasp.py:725 skills/igv-validator/igv_validator.py:1411 and 15 more
- 12,505 network referencesin 320 files: skills/gwas-lookup/tests/fixtures/gwas_catalog_v2_rs7903146_page0.json:43 skills/gwas-lookup/tests/fixtures/gwas_catalog_v2_rs7903146_page1.json:45 skills/clinical-trial-finder/examples/demo_output/fhir_bundle.json:6 and 317 more
- 10 obfuscation signalsin 4 files: skills/data-extractor/data_extractor_core/digitizer.py:930 skills/bioqc-mcp/bioqc_mcp.py:1180 skills/data-extractor/web/server.py:247 and 1 more
- No instruction overrides
- 1,128 executable scriptsin 536 files: clawbio.py:1 skills/pharmgx-reporter/pharmgx_reporter.py:1 skills/analyze-fasta/analyze_fasta.py:1 and 533 more
- 637 references to secretsin 88 files: docs/data-handling.md:71 skills/illumina-bridge/tests/test_illumina_bridge.py:48 skills/protocols-io/tests/test_protocols_io.py:30 and 85 more
- No requests to vote in Hot
Show all 14,340 signals by file
.claude-plugin/marketplace.json
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{ "$schema": "https://anthropic.com/claude-code/marketplace.schema.json", - Network accessline 2
"$schema": "https://anthropic.com/claude-code/marketplace.schema.json", - Network accessline 19
"email": "mc@manuelcorpas.com" }, "homepage": "https://clawbio.ai", - Network accessline 20
}, "homepage": "https://clawbio.ai", "repository": "https://github.com/ClawBio/ClawBio", - Network accessline 21
"homepage": "https://clawbio.ai", - Network accessline 22
"repository": "https://github.com/ClawBio/ClawBio",
.claude-plugin/plugin.json
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"email": "mc@manuelcorpas.com" }, "homepage": "https://clawbio.ai", - Network accessline 8
}, "homepage": "https://clawbio.ai", "repository": "https://github.com/ClawBio/ClawBio", - Network accessline 9
"homepage": "https://clawbio.ai", - Network accessline 10
"repository": "https://github.com/ClawBio/ClawBio",
clawbio.py
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docs/data-handling.md
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keys are always sent, so an identifier put in a skill or attribute *name* is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local - Network accessline 28
keys are always sent, so an identifier put in a skill or attribute *name* is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local - Network accessline 28
keys are always sent, so an identifier put in a skill or attribute *name* is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local - Network accessline 28
keys are always sent, so an identifier put in a skill or attribute *name* is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local - Network accessline 28
keys are always sent, so an identifier put in a skill or attribute *name* is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local - Network accessline 29
is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local collector (Phoenix, say) keeps all of it on this machine; a remote one does - Network accessline 29
is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local collector (Phoenix, say) keeps all of it on this machine; a remote one does - Network accessline 29
is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local collector (Phoenix, say) keeps all of it on this machine; a remote one does - Network accessline 29
is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local collector (Phoenix, say) keeps all of it on this machine; a remote one does - Network accessline 29
is outside their reach. The transport is plain OTLP/HTTP, so point the variable at a collector on this machine or at an `https://` URL. A local collector (Phoenix, say) keeps all of it on this machine; a remote one does - Network accessline 30
variable at a collector on this machine or at an `https://` URL. A local - Network accessline 30
variable at a collector on this machine or at an `https://` URL. A local - Network accessline 30
variable at a collector on this machine or at an `https://` URL. A local - Network accessline 30
variable at a collector on this machine or at an `https://` URL. A local - Network accessline 30
variable at a collector on this machine or at an `https://` URL. A local - Access to secretsline 71
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**This is not a port problem, and opening FTP ports will not fix it.** Despite the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 131
**This is not a port problem, and opening FTP ports will not fix it.** Despite the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 131
**This is not a port problem, and opening FTP ports will not fix it.** Despite the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 131
**This is not a port problem, and opening FTP ports will not fix it.** Despite the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 131
**This is not a port problem, and opening FTP ports will not fix it.** Despite the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 132
the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is opened, so all traffic is ordinary **HTTPS on TCP/443**. What differs is the - Network accessline 132
the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is opened, so all traffic is ordinary **HTTPS on TCP/443**. What differs is the - Network accessline 132
the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is opened, so all traffic is ordinary **HTTPS on TCP/443**. What differs is the - Network accessline 132
the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is opened, so all traffic is ordinary **HTTPS on TCP/443**. What differs is the - Network accessline 132
the `ftp.*` hostnames, these skills never speak the FTP protocol: every `ftp://` URL an archive advertises is rewritten to `https://` before it is opened, so all traffic is ordinary **HTTPS on TCP/443**. What differs is the - Network accessline 133
`ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 133
`ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 133
`ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 133
`ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 133
`ftp://` URL an archive advertises is rewritten to `https://` before it is - Network accessline 157
for h in www.ebi.ac.uk ftp.ebi.ac.uk ftp.sra.ebi.ac.uk ftp.pride.ebi.ac.uk \ eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https:/ - Network accessline 157
for h in www.ebi.ac.uk ftp.ebi.ac.uk ftp.sra.ebi.ac.uk ftp.pride.ebi.ac.uk \ eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https:/ - Network accessline 157
for h in www.ebi.ac.uk ftp.ebi.ac.uk ftp.sra.ebi.ac.uk ftp.pride.ebi.ac.uk \ eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https:/ - Network accessline 157
for h in www.ebi.ac.uk ftp.ebi.ac.uk ftp.sra.ebi.ac.uk ftp.pride.ebi.ac.uk \ eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https:/ - Network accessline 157
for h in www.ebi.ac.uk ftp.ebi.ac.uk ftp.sra.ebi.ac.uk ftp.pride.ebi.ac.uk \ eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https:/ - Network accessline 158
eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" done - Network accessline 158
eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" done - Network accessline 158
eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" done - Network accessline 158
eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" done - Network accessline 158
eutils.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov ftp.ncbi.nlm.nih.gov; do printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" done - Network accessline 159
printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" - Network accessline 159
printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" - Network accessline 159
printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" - Network accessline 159
printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" - Network accessline 159
printf '%-26s %s\n' "$h" "$(curl -sS -o /dev/null -m 15 -w '%{http_code}' "https://$h/" 2>&1)" - Network accessline 165
default**; `--tool wget` is the alternative, and both resume a dropped multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 165
default**; `--tool wget` is the alternative, and both resume a dropped multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 165
default**; `--tool wget` is the alternative, and both resume a dropped multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 165
default**; `--tool wget` is the alternative, and both resume a dropped multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 165
default**; `--tool wget` is the alternative, and both resume a dropped multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 166
multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file produced `206 Partial Content`, only the remainder was transferred, and the - Network accessline 166
multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file produced `206 Partial Content`, only the remainder was transferred, and the - Network accessline 166
multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file produced `206 Partial Content`, only the remainder was transferred, and the - Network accessline 166
multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file produced `206 Partial Content`, only the remainder was transferred, and the - Network accessline 166
multi-gigabyte transfer rather than restarting it (`-C -` for curl, `-c` for wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file produced `206 Partial Content`, only the remainder was transferred, and the - Network accessline 167
wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 167
wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 167
wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 167
wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 167
wget — verified against GNU Wget 1.25.0 on 2026-09-23: a truncated file - Network accessline 172
curl is the default for the two things wget cannot do. It aborts a transfer - Network accessline 172
curl is the default for the two things wget cannot do. It aborts a transfer - Network accessline 172
curl is the default for the two things wget cannot do. It aborts a transfer - Network accessline 172
curl is the default for the two things wget cannot do. It aborts a transfer - Network accessline 172
curl is the default for the two things wget cannot do. It aborts a transfer - Network accessline 175
under a burst of requests, and which a plain `--retry` does not cover. `--retry-all-errors` is probed for at run time rather than hardcoded, because it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 175
under a burst of requests, and which a plain `--retry` does not cover. `--retry-all-errors` is probed for at run time rather than hardcoded, because it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 175
under a burst of requests, and which a plain `--retry` does not cover. `--retry-all-errors` is probed for at run time rather than hardcoded, because it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 175
under a burst of requests, and which a plain `--retry` does not cover. `--retry-all-errors` is probed for at run time rather than hardcoded, because it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 175
under a burst of requests, and which a plain `--retry` does not cover. `--retry-all-errors` is probed for at run time rather than hardcoded, because it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 177
it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 177
it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 177
it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 177
it needs curl >= 7.71 and older clusters ship 7.29. - Network accessline 177
it needs curl >= 7.71 and older clusters ship 7.29. - Access to secretsline 189
[Credential-related source omitted] - Access to secretsline 189
[Credential-related source omitted] - Access to secretsline 189
[Credential-related source omitted] - Access to secretsline 189
[Credential-related source omitted] - Access to secretsline 189
[Credential-related source omitted] - Access to secretsline 190
[Credential-related source omitted] - Access to secretsline 190
[Credential-related source omitted] - Access to secretsline 190
[Credential-related source omitted] - Access to secretsline 190
[Credential-related source omitted] - Access to secretsline 190
[Credential-related source omitted]
scripts/generate_catalog.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/affinity-proteomics/SKILL.md
- Network accessline 22
always: false emoji: 🧪 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
emoji: 🧪 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
homepage: https://github.com/ClawBio/ClawBio - Network accessline 184
- [Assarsson et al. (2014)](https://pubmed.ncbi.nlm.nih.gov/25057488/) — Olink PEA technology - Network accessline 185
- [Gold et al. (2010)](https://pubmed.ncbi.nlm.nih.gov/20829826/) — SOMAmer aptamer technology - Network accessline 186
- [OlinkAnalyze](https://cran.r-project.org/package=OlinkAnalyze) — Official Olink R toolkit - Network accessline 187
- [somadata](https://pypi.org/project/somadata/) — Python ADAT parser
skills/affinity-proteomics/affinity_proteomics.py
- Executable scriptline 1
#!/usr/bin/env python3
skills/affinity-proteomics/tests/__init__.py
- Executable scriptline 1
Executable file
skills/affinity-proteomics/tests/test_affinity_proteomics.py
- Executable scriptline 1
Executable file
skills/analyze-fasta/SKILL.md
- Network accessline 64
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 64
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 65
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 65
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 66
homepage: https://github.com/ClawBio/ClawBio - Network accessline 66
homepage: https://github.com/ClawBio/ClawBio - Network accessline 295
- [Biopython](https://biopython.org/) — sequence parsing, GC, molecular weight, ProtParam. - Network accessline 295
- [Biopython](https://biopython.org/) — sequence parsing, GC, molecular weight, ProtParam. - Network accessline 296
- [Cock et al. 2009, Bioinformatics 25(11):1422](https://doi.org/10.1093/bioinformatics/btp163) — Biopython reference. - Network accessline 296
- [Cock et al. 2009, Bioinformatics 25(11):1422](https://doi.org/10.1093/bioinformatics/btp163) — Biopython reference. - Network accessline 297
- [Kyte & Doolittle 1982, J Mol Biol 157:105](https://doi.org/10.1016/0022-2836\(82\)90515-0) — GRAVY index definition. - Network accessline 297
- [Kyte & Doolittle 1982, J Mol Biol 157:105](https://doi.org/10.1016/0022-2836\(82\)90515-0) — GRAVY index definition.
skills/analyze-fasta/analyze_fasta.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 503
<title>Analisis FASTA - {html_mod.escape(report['file'])}</title> <style> @import url('https://fonts.googleapis.com/css2?family=Merriweather:wght@400;700;900&family=Source+Sans+3:wght@300;400;500;600;700&family=JetBrains+Mono:wg - Network accessline 503
<title>Analisis FASTA - {html_mod.escape(report['file'])}</title> <style> @import url('https://fonts.googleapis.com/css2?family=Merriweather:wght@400;700;900&family=Source+Sans+3:wght@300;400;500;600;700&family=JetBrains+Mono:wg - Network accessline 504
<style> @import url('https://fonts.googleapis.com/css2?family=Merriweather:wght@400;700;900&family=Source+Sans+3:wght@300;400;500;600;700&family=JetBrains+Mono:wght@400;500&display=swap'); :root {{ - Network accessline 504
<style> @import url('https://fonts.googleapis.com/css2?family=Merriweather:wght@400;700;900&family=Source+Sans+3:wght@300;400;500;600;700&family=JetBrains+Mono:wght@400;500&display=swap'); :root {{ - Network accessline 505
@import url('https://fonts.googleapis.com/css2?family=Merriweather:wght@400;700;900&family=Source+Sans+3:wght@300;400;500;600;700&family=JetBrains+Mono:wght@400;500&display=swap'); - Network accessline 505
@import url('https://fonts.googleapis.com/css2?family=Merriweather:wght@400;700;900&family=Source+Sans+3:wght@300;400;500;600;700&family=JetBrains+Mono:wght@400;500&display=swap');
skills/analyze-fasta/tests/test_analyze_fasta.py
skills/ancestry-risk-profiler/SKILL.md
- Network accessline 76
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 76
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 77
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 77
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 78
homepage: https://github.com/ClawBio/ClawBio - Network accessline 78
homepage: https://github.com/ClawBio/ClawBio - Network accessline 336
- Genovese et al. (2010) Science 329:841. PMID 20566908. APOL1 G1/G2 kidney disease (recessive compound model) - Karczewski et al. (2020) Nature 581:434. PMID 32461654. gnomAD v3.1 allele frequencies for AISNP panel - Nassir et al. (2009) B - Network accessline 336
- Genovese et al. (2010) Science 329:841. PMID 20566908. APOL1 G1/G2 kidney disease (recessive compound model) - Karczewski et al. (2020) Nature 581:434. PMID 32461654. gnomAD v3.1 allele frequencies for AISNP panel - Nassir et al. (2009) B - Network accessline 337
- Karczewski et al. (2020) Nature 581:434. PMID 32461654. gnomAD v3.1 allele frequencies for AISNP panel - Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). DOI 10.1186/1471-2156-10-39. 93 - Network accessline 337
- Karczewski et al. (2020) Nature 581:434. PMID 32461654. gnomAD v3.1 allele frequencies for AISNP panel - Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). DOI 10.1186/1471-2156-10-39. 93 - Network accessline 338
- Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). DOI 10.1186/1471-2156-10-39. 93 AISNP panel for continental ancestry inference; does not validate a low-coverage implementation shortcut - Network accessline 338
- Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). DOI 10.1186/1471-2156-10-39. 93 AISNP panel for continental ancestry inference; does not validate a low-coverage implementation shortcut - Network accessline 339
- Kosoy et al. (2009) Human Mutation 30(1):69–78. [PMID 18683858](https://pubmed.ncbi.nlm.nih.gov/18683858/). DOI 10.1002/humu.20822. 128-marker AISNP set and 96/64/48/24-marker subsets; does not define this software's global Fst ≥ 0.3 gate - Network accessline 339
- Kosoy et al. (2009) Human Mutation 30(1):69–78. [PMID 18683858](https://pubmed.ncbi.nlm.nih.gov/18683858/). DOI 10.1002/humu.20822. 128-marker AISNP set and 96/64/48/24-marker subsets; does not define this software's global Fst ≥ 0.3 gate
skills/ancestry-risk-profiler/ancestry_risk_profiler.py
skills/ancestry-risk-profiler/data/PROVENANCE.md
- Network accessline 25
Reference context: - Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). - Network accessline 25
Reference context: - Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). - Network accessline 26
- Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). - Network accessline 26
- Nassir et al. (2009) BMC Genetics 10:39. [PMID 19630973](https://pubmed.ncbi.nlm.nih.gov/19630973/). - Network accessline 27
Evaluated a 93-SNP AIM panel for continental ancestry inference. - Kosoy et al. (2009) Human Mutation 30(1):69–78. [PMID 18683858](https://pubmed.ncbi.nlm.nih.gov/18683858/). Described a 128-marker AIM set and smaller subsets down to 24 m - Network accessline 27
Evaluated a 93-SNP AIM panel for continental ancestry inference. - Kosoy et al. (2009) Human Mutation 30(1):69–78. [PMID 18683858](https://pubmed.ncbi.nlm.nih.gov/18683858/). Described a 128-marker AIM set and smaller subsets down to 24 m - Network accessline 28
- Kosoy et al. (2009) Human Mutation 30(1):69–78. [PMID 18683858](https://pubmed.ncbi.nlm.nih.gov/18683858/). - Network accessline 28
- Kosoy et al. (2009) Human Mutation 30(1):69–78. [PMID 18683858](https://pubmed.ncbi.nlm.nih.gov/18683858/).
skills/ancestry-risk-profiler/tests/test_ancestry_reproducibility.py
skills/ancestry-risk-profiler/tests/test_ancestry_risk_profiler.py
skills/archaic-introgression/SKILL.md
- Network accessline 25
always: false emoji: 🦴 homepage: https://github.com/ClawBio/ClawBio - Network accessline 25
always: false emoji: 🦴 homepage: https://github.com/ClawBio/ClawBio - Network accessline 26
emoji: 🦴 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 26
emoji: 🦴 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 27
homepage: https://github.com/ClawBio/ClawBio - Network accessline 27
homepage: https://github.com/ClawBio/ClawBio
skills/archaic-introgression/archaic_introgression.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 42
[Credential-related source omitted] - Access to secretsline 42
[Credential-related source omitted]
skills/archaic-introgression/pipeline.py
skills/archaic-introgression/tests/__init__.py
skills/archaic-introgression/tests/test_archaic_introgression.py
skills/archaic-introgression/tests/test_pipeline.py
skills/arrayexpress-fetch/SKILL.md
- Network accessline 75
always: false emoji: "🧫" homepage: https://www.ebi.ac.uk/biostudies/arrayexpress - Network accessline 75
always: false emoji: "🧫" homepage: https://www.ebi.ac.uk/biostudies/arrayexpress - Network accessline 76
emoji: "🧫" homepage: https://www.ebi.ac.uk/biostudies/arrayexpress os: - Network accessline 76
emoji: "🧫" homepage: https://www.ebi.ac.uk/biostudies/arrayexpress os: - Network accessline 77
homepage: https://www.ebi.ac.uk/biostudies/arrayexpress - Network accessline 77
homepage: https://www.ebi.ac.uk/biostudies/arrayexpress - Network accessline 308
sample,fastq_1,fastq_2 Sample_1,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R1.fastq.gz,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R2.fastq.gz - Network accessline 308
sample,fastq_1,fastq_2 Sample_1,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R1.fastq.gz,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R2.fastq.gz - Network accessline 309
Sample_1,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R1.fastq.gz,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R2.fastq.gz - Network accessline 309
Sample_1,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R1.fastq.gz,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S1_R2.fastq.gz - Network accessline 310
Sample_2,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S2_R1.fastq.gz,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S2_R2.fastq.gz - Network accessline 310
Sample_2,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S2_R1.fastq.gz,https://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MTAB/E-MTAB-10030/B1_S2_R2.fastq.gz - Network accessline 356
later with a missing-file error rather than being rejected up front. - **Gotcha 4**: You will want to hardcode `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. Do not. It works — - Network accessline 356
later with a missing-file error rather than being rejected up front. - **Gotcha 4**: You will want to hardcode `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. Do not. It works — - Network accessline 357
- **Gotcha 4**: You will want to hardcode `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. Do not. It works — it 302-redirects — but there is no one base tree behind it, and the redirect - Network accessline 357
- **Gotcha 4**: You will want to hardcode `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. Do not. It works — it 302-redirects — but there is no one base tree behind it, and the redirect - Network accessline 358
`https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. Do not. It works — - Network accessline 358
`https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. Do not. It works — - Network accessline 376
host and clears on retry (observed 2026-09-22). Generated download scripts handle this themselves: `--tool curl` emits `--retry 5 --retry-delay 10` plus `--retry-all-errors` where curl supports it. In-process `--command download` - Network accessline 376
host and clears on retry (observed 2026-09-22). Generated download scripts handle this themselves: `--tool curl` emits `--retry 5 --retry-delay 10` plus `--retry-all-errors` where curl supports it. In-process `--command download` - Network accessline 377
handle this themselves: `--tool curl` emits `--retry 5 --retry-delay 10` plus `--retry-all-errors` where curl supports it. In-process `--command download` does not retry on 403, so just re-run it. - Network accessline 377
handle this themselves: `--tool curl` emits `--retry 5 --retry-delay 10` plus `--retry-all-errors` where curl supports it. In-process `--command download` does not retry on 403, so just re-run it. - Network accessline 378
`--retry-all-errors` where curl supports it. In-process `--command download` - Network accessline 378
`--retry-all-errors` where curl supports it. In-process `--command download` - Network accessline 481
- **Ported from** [`UKDRI/informatics_data_skills`](https://github.com/UKDRI/informatics_data_skills) - Network accessline 481
- **Ported from** [`UKDRI/informatics_data_skills`](https://github.com/UKDRI/informatics_data_skills) - Network accessline 482
[`UKDRI/informatics_data_skills`](https://github.com/UKDRI/informatics_data_skills) - Network accessline 482
[`UKDRI/informatics_data_skills`](https://github.com/UKDRI/informatics_data_skills) - Network accessline 485
- **ArrayExpress / BioStudies**: Sarkans et al. (2018) *The BioStudies database — one stop shop for all data supporting a life sciences study.* Nucleic Acids Research 46(D1):D1266–D1270. <https://doi.org/10.1093/nar/gkx965> - Network accessline 485
- **ArrayExpress / BioStudies**: Sarkans et al. (2018) *The BioStudies database — one stop shop for all data supporting a life sciences study.* Nucleic Acids Research 46(D1):D1266–D1270. <https://doi.org/10.1093/nar/gkx965> - Network accessline 486
one stop shop for all data supporting a life sciences study.* Nucleic Acids Research 46(D1):D1266–D1270. <https://doi.org/10.1093/nar/gkx965> - **Demo fixture**: E-MTAB-10030, "Single-cell RNA-seq of rat microglia in - Network accessline 486
one stop shop for all data supporting a life sciences study.* Nucleic Acids Research 46(D1):D1266–D1270. <https://doi.org/10.1093/nar/gkx965> - **Demo fixture**: E-MTAB-10030, "Single-cell RNA-seq of rat microglia in - Network accessline 487
Research 46(D1):D1266–D1270. <https://doi.org/10.1093/nar/gkx965> - Network accessline 487
Research 46(D1):D1266–D1270. <https://doi.org/10.1093/nar/gkx965> - Network accessline 493
- **MAGE-TAB**: Rayner et al. (2006) *A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.* BMC Bioinformatics 7:489. <https://doi.org/10.1186/1471-2105-7-489> - Network accessline 493
- **MAGE-TAB**: Rayner et al. (2006) *A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.* BMC Bioinformatics 7:489. <https://doi.org/10.1186/1471-2105-7-489> - Network accessline 495
<https://doi.org/10.1186/1471-2105-7-489> - Network accessline 495
<https://doi.org/10.1186/1471-2105-7-489>
skills/arrayexpress-fetch/arrayexpress_fetch.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 214
output_dir, title=f"ArrayExpress report — {accession}", source_url=f"[EMBL-EBI ArrayExpress](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/{accession})", - Network accessline 214
output_dir, title=f"ArrayExpress report — {accession}", source_url=f"[EMBL-EBI ArrayExpress](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/{accession})", - Network accessline 215
title=f"ArrayExpress report — {accession}", source_url=f"[EMBL-EBI ArrayExpress](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/{accession})", sections=sections, - Network accessline 215
title=f"ArrayExpress report — {accession}", source_url=f"[EMBL-EBI ArrayExpress](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/{accession})", sections=sections, - Network accessline 216
source_url=f"[EMBL-EBI ArrayExpress](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/{accession})", - Network accessline 216
source_url=f"[EMBL-EBI ArrayExpress](https://www.ebi.ac.uk/biostudies/arrayexpress/studies/{accession})",
skills/arrayexpress-fetch/arrayexpress_fetch_api.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
ArrayExpress is now the functional-genomics collection inside BioStudies, so this uses the BioStudies REST API (https://www.ebi.ac.uk/biostudies/api/v1) with - Network accessline 8
ArrayExpress is now the functional-genomics collection inside BioStudies, so this uses the BioStudies REST API (https://www.ebi.ac.uk/biostudies/api/v1) with - Network accessline 9
uses the BioStudies REST API (https://www.ebi.ac.uk/biostudies/api/v1) with - Network accessline 9
uses the BioStudies REST API (https://www.ebi.ac.uk/biostudies/api/v1) with - Network accessline 35
API = "https://www.ebi.ac.uk/biostudies/api/v1" - Network accessline 35
API = "https://www.ebi.ac.uk/biostudies/api/v1" - Network accessline 36
FILES = "https://www.ebi.ac.uk/biostudies/files" - Network accessline 36
FILES = "https://www.ebi.ac.uk/biostudies/files" - Network accessline 43
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 43
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 44
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 44
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 45
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 45
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 46
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 46
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 155
DIVERGES FROM UPSTREAM, deliberately, and identically to biostudies-fetch. Upstream hardcodes `https://www.ebi.ac.uk/biostudies/files/{acc}/{path}`. - Network accessline 155
DIVERGES FROM UPSTREAM, deliberately, and identically to biostudies-fetch. Upstream hardcodes `https://www.ebi.ac.uk/biostudies/files/{acc}/{path}`. - Network accessline 156
Upstream hardcodes `https://www.ebi.ac.uk/biostudies/files/{acc}/{path}`. - Network accessline 156
Upstream hardcodes `https://www.ebi.ac.uk/biostudies/files/{acc}/{path}`. - Network accessline 195
return print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(file_url(accession, path), headers={"User-Agent": USER_AGENT}) - Network accessline 195
return print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(file_url(accession, path), headers={"User-Agent": USER_AGENT}) - Network accessline 196
print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(file_url(accession, path), headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 196
print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(file_url(accession, path), headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 197
req = urllib.request.Request(file_url(accession, path), headers={"User-Agent": USER_AGENT}) - Network accessline 197
req = urllib.request.Request(file_url(accession, path), headers={"User-Agent": USER_AGENT}) - Network accessline 198
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 198
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 233
ENA_PORTAL = "https://www.ebi.ac.uk/ena/portal/api" - Network accessline 233
ENA_PORTAL = "https://www.ebi.ac.uk/ena/portal/api" - Network accessline 292
`ftp://` is rewritten (these skills never speak FTP), `http(s)://` passes through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 292
`ftp://` is rewritten (these skills never speak FTP), `http(s)://` passes through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 293
through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 293
through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 692
try: data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 692
try: data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 693
data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) .decode("utf-8", "replace")) - Network accessline 693
data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) .decode("utf-8", "replace")) - Network accessline 694
http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 694
http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession)
skills/arrayexpress-fetch/examples/demo_E-MTAB-10030.json
- Network accessline 325
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419-ERS5592421" - Network accessline 325
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419-ERS5592421" - Network accessline 326
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419-ERS5592421" } - Network accessline 326
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419-ERS5592421" } - Network accessline 327
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419-ERS5592421" - Network accessline 327
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419-ERS5592421" - Network accessline 345
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422-ERS5592424" - Network accessline 345
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422-ERS5592424" - Network accessline 346
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422-ERS5592424" } - Network accessline 346
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422-ERS5592424" } - Network accessline 347
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422-ERS5592424" - Network accessline 347
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422-ERS5592424" - Network accessline 463
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419" - Network accessline 463
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419" - Network accessline 464
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419" } - Network accessline 464
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419" } - Network accessline 465
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419" - Network accessline 465
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592419" - Network accessline 495
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592420" - Network accessline 495
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592420" - Network accessline 496
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592420" } - Network accessline 496
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592420" } - Network accessline 497
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592420" - Network accessline 497
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592420" - Network accessline 527
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592421" - Network accessline 527
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592421" - Network accessline 528
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592421" } - Network accessline 528
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592421" } - Network accessline 529
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592421" - Network accessline 529
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592421" - Network accessline 559
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422" - Network accessline 559
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422" - Network accessline 560
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422" } - Network accessline 560
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422" } - Network accessline 561
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422" - Network accessline 561
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592422" - Network accessline 591
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592423" - Network accessline 591
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592423" - Network accessline 592
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592423" } - Network accessline 592
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592423" } - Network accessline 593
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592423" - Network accessline 593
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592423" - Network accessline 623
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592424" - Network accessline 623
{ "name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592424" - Network accessline 624
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592424" } - Network accessline 624
"name": "url", "value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592424" } - Network accessline 625
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592424" - Network accessline 625
"value": "https://www.ebi.ac.uk/ena/browser/view/ERS5592424"
skills/arrayexpress-fetch/tests/test_arrayexpress_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 82
TO_HTTPS_CASES = [ ("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 82
TO_HTTPS_CASES = [ ("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 83
("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 83
("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 84
("https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 84
("https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 85
("http://example.org/x.fastq.gz", "http://example.org/x.fastq.gz"), - Network accessline 85
("http://example.org/x.fastq.gz", "http://example.org/x.fastq.gz"), - Network accessline 87
("ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 87
("ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 144
assert api.to_https("ftp://ftp.ebi.ac.uk/x.gz") == "https://ftp.ebi.ac.uk/x.gz" - Network accessline 144
assert api.to_https("ftp://ftp.ebi.ac.uk/x.gz") == "https://ftp.ebi.ac.uk/x.gz" - Network accessline 170
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030"} - Network accessline 170
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030"} - Network accessline 172
url = api.file_url(DEMO_ACCESSION, "E-MTAB-10030.sdrf.txt") assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030" - Network accessline 172
url = api.file_url(DEMO_ACCESSION, "E-MTAB-10030.sdrf.txt") assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030" - Network accessline 173
assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030" "/Files/E-MTAB-10030.sdrf.txt" - Network accessline 173
assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030" "/Files/E-MTAB-10030.sdrf.txt" - Network accessline 174
"https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030" - Network accessline 174
"https://ftp.ebi.ac.uk/biostudies/fire/E-MTAB-/030/E-MTAB-10030" - Network accessline 181
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/E-M/001/E-MTAB-1"} - Network accessline 181
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/E-M/001/E-MTAB-1"} - Network accessline 191
@pytest.mark.parametrize("link", [ "https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 191
@pytest.mark.parametrize("link", [ "https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 192
"https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 192
"https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 193
"http://ftp.ebi.ac.uk/x", "file:///etc", - Network accessline 193
"http://ftp.ebi.ac.uk/x", "file:///etc", - Network accessline 288
with patch("urllib.request.urlopen", - Network accessline 288
with patch("urllib.request.urlopen", - Network accessline 332
with patch.object(api, "http_get", return_value=sdrf), \ patch.object(api, "file_url", return_value="https://example/x.sdrf.txt"), \ - Network accessline 332
with patch.object(api, "http_get", return_value=sdrf), \ patch.object(api, "file_url", return_value="https://example/x.sdrf.txt"), \ - Network accessline 333
patch.object(api, "file_url", return_value="https://example/x.sdrf.txt"), \ - Network accessline 333
patch.object(api, "file_url", return_value="https://example/x.sdrf.txt"), \ - Network accessline 394
"S1\tERR1\tS1_1.fastq.gz\n" "S1\tERR1\tS1_2.fastq.gz\n") ena = ["https://ftp.sra.ebi.ac.uk/vol1/ERR1_1.fastq.gz", - Network accessline 394
"S1\tERR1\tS1_1.fastq.gz\n" "S1\tERR1\tS1_2.fastq.gz\n") ena = ["https://ftp.sra.ebi.ac.uk/vol1/ERR1_1.fastq.gz", - Network accessline 395
"S1\tERR1\tS1_2.fastq.gz\n") ena = ["https://ftp.sra.ebi.ac.uk/vol1/ERR1_1.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/ERR1_2.fastq.gz"] - Network accessline 395
"S1\tERR1\tS1_2.fastq.gz\n") ena = ["https://ftp.sra.ebi.ac.uk/vol1/ERR1_1.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/ERR1_2.fastq.gz"] - Network accessline 396
ena = ["https://ftp.sra.ebi.ac.uk/vol1/ERR1_1.fastq.gz", - Network accessline 396
ena = ["https://ftp.sra.ebi.ac.uk/vol1/ERR1_1.fastq.gz", - Network accessline 397
"https://ftp.sra.ebi.ac.uk/vol1/ERR1_2.fastq.gz"] - Network accessline 397
"https://ftp.sra.ebi.ac.uk/vol1/ERR1_2.fastq.gz"]
skills/article-data-fetcher/SKILL.md
- Network accessline 81
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 81
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 82
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 82
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 83
homepage: https://github.com/ClawBio/ClawBio - Network accessline 83
homepage: https://github.com/ClawBio/ClawBio - Network accessline 160
| DOI | `10.xxxx/xxxxx` | `10.1038/s41586-021-03819-2` | | PubMed ID | `PMID:xxxxxxxx` or bare integer | `34613072` | | Repository URL | Direct URL to GEO/ENA/Zenodo page | `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456` | - Network accessline 160
| DOI | `10.xxxx/xxxxx` | `10.1038/s41586-021-03819-2` | | PubMed ID | `PMID:xxxxxxxx` or bare integer | `34613072` | | Repository URL | Direct URL to GEO/ENA/Zenodo page | `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456` | - Network accessline 161
| PubMed ID | `PMID:xxxxxxxx` or bare integer | `34613072` | | Repository URL | Direct URL to GEO/ENA/Zenodo page | `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456` | | File types | Comma-separated extensions | `vcf,fasta,h5ad - Network accessline 161
| PubMed ID | `PMID:xxxxxxxx` or bare integer | `34613072` | | Repository URL | Direct URL to GEO/ENA/Zenodo page | `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456` | | File types | Comma-separated extensions | `vcf,fasta,h5ad - Network accessline 162
| Repository URL | Direct URL to GEO/ENA/Zenodo page | `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456` | - Network accessline 162
| Repository URL | Direct URL to GEO/ENA/Zenodo page | `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456` | - Network accessline 324
{ "filename": "matrix.h5ad", "source_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/...", - Network accessline 324
{ "filename": "matrix.h5ad", "source_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/...", - Network accessline 325
"filename": "matrix.h5ad", "source_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/...", "repository": "GEO", - Network accessline 325
"filename": "matrix.h5ad", "source_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/...", "repository": "GEO", - Network accessline 326
"source_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/...", - Network accessline 326
"source_url": "https://ftp.ncbi.nlm.nih.gov/geo/series/...", - Network accessline 388
- [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/); Gene Expression Omnibus FTP and Entrez API - Network accessline 388
- [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/); Gene Expression Omnibus FTP and Entrez API - Network accessline 389
- [ENA Portal API](https://www.ebi.ac.uk/ena/portal/api/); European Nucleotide Archive file listings - Network accessline 389
- [ENA Portal API](https://www.ebi.ac.uk/ena/portal/api/); European Nucleotide Archive file listings - Network accessline 390
- [Zenodo REST API](https://developers.zenodo.org/); Open-access research data repository - Network accessline 390
- [Zenodo REST API](https://developers.zenodo.org/); Open-access research data repository - Network accessline 391
- [Figshare API](https://docs.figshare.com/); Scientific data and figure repository - Network accessline 391
- [Figshare API](https://docs.figshare.com/); Scientific data and figure repository - Network accessline 392
- [Dryad API](https://datadryad.org/api/v2/docs/); Curated data repository for research publications - Network accessline 392
- [Dryad API](https://datadryad.org/api/v2/docs/); Curated data repository for research publications - Network accessline 393
- [BioStudies API](https://www.ebi.ac.uk/biostudies/); ArrayExpress and EBI study data - Network accessline 393
- [BioStudies API](https://www.ebi.ac.uk/biostudies/); ArrayExpress and EBI study data
skills/article-data-fetcher/article_data_fetcher.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 43
ENTREZ_BASE = "https://edata.ncbi.nlm.nih.gov/geo/query/acc.cgi" - Network accessline 43
ENTREZ_BASE = "https://edata.ncbi.nlm.nih.gov/geo/query/acc.cgi" - Network accessline 44
CROSSREF_BASE = "https://api.crossref.org/works" - Network accessline 44
CROSSREF_BASE = "https://api.crossref.org/works" - Network accessline 45
ENA_PORTAL = "https://www.ebi.ac.uk/ena/portal/api/filereport" - Network accessline 45
ENA_PORTAL = "https://www.ebi.ac.uk/ena/portal/api/filereport" - Network accessline 46
ZENODO_BASE = "https://zenodo.org/api/records" - Network accessline 46
ZENODO_BASE = "https://zenodo.org/api/records" - Network accessline 47
FIGSHARE_BASE = "https://api.figshare.com/v2/articles" - Network accessline 47
FIGSHARE_BASE = "https://api.figshare.com/v2/articles" - Network accessline 69
url = f"{CROSSREF_BASE}/{doi}" r = requests.get(url, timeout=15, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 69
url = f"{CROSSREF_BASE}/{doi}" r = requests.get(url, timeout=15, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 70
r = requests.get(url, timeout=15, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 70
r = requests.get(url, timeout=15, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 83
url = ( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 83
url = ( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 84
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 84
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 85
f"?db=pubmed&id={pmid}&retmode=json" ) r = requests.get(url, timeout=15) - Network accessline 85
f"?db=pubmed&id={pmid}&retmode=json" ) r = requests.get(url, timeout=15) - Network accessline 86
) r = requests.get(url, timeout=15) r.raise_for_status() - Network accessline 86
) r = requests.get(url, timeout=15) r.raise_for_status() - Network accessline 87
r = requests.get(url, timeout=15) - Network accessline 87
r = requests.get(url, timeout=15) - Network accessline 115
try: summary_url = ( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 115
try: summary_url = ( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 116
summary_url = ( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" f"?db=pmc&id={numeric_id}&retmode=json" - Network accessline 116
summary_url = ( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" f"?db=pmc&id={numeric_id}&retmode=json" - Network accessline 117
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 117
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 118
f"?db=pmc&id={numeric_id}&retmode=json" ) r = requests.get(summary_url, timeout=15) - Network accessline 118
f"?db=pmc&id={numeric_id}&retmode=json" ) r = requests.get(summary_url, timeout=15) - Network accessline 119
) r = requests.get(summary_url, timeout=15) if r.status_code == 200: - Network accessline 119
) r = requests.get(summary_url, timeout=15) if r.status_code == 200: - Network accessline 120
r = requests.get(summary_url, timeout=15) - Network accessline 120
r = requests.get(summary_url, timeout=15) - Network accessline 130
doi = None try: page_url = f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" - Network accessline 130
doi = None try: page_url = f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" - Network accessline 131
try: page_url = f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" r = requests.get(page_url, timeout=20, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 131
try: page_url = f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" r = requests.get(page_url, timeout=20, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 132
page_url = f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" r = requests.get(page_url, timeout=20, headers={"User-Agent": "ClawBio/1.0"}) if r.status_code == 200: - Network accessline 132
page_url = f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" r = requests.get(page_url, timeout=20, headers={"User-Agent": "ClawBio/1.0"}) if r.status_code == 200: - Network accessline 133
r = requests.get(page_url, timeout=20, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 133
r = requests.get(page_url, timeout=20, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 183
raise ValueError( f"Cannot recognise identifier '{identifier}'. " "Provide a DOI (10.xxxx/… or https://doi.org/…), PMID, PMCID (e.g. PMC1234567), or repository URL." - Network accessline 183
raise ValueError( f"Cannot recognise identifier '{identifier}'. " "Provide a DOI (10.xxxx/… or https://doi.org/…), PMID, PMCID (e.g. PMC1234567), or repository URL." - Network accessline 184
f"Cannot recognise identifier '{identifier}'. " "Provide a DOI (10.xxxx/… or https://doi.org/…), PMID, PMCID (e.g. PMC1234567), or repository URL." ) - Network accessline 184
f"Cannot recognise identifier '{identifier}'. " "Provide a DOI (10.xxxx/… or https://doi.org/…), PMID, PMCID (e.g. PMC1234567), or repository URL." ) - Network accessline 185
"Provide a DOI (10.xxxx/… or https://doi.org/…), PMID, PMCID (e.g. PMC1234567), or repository URL." - Network accessline 185
"Provide a DOI (10.xxxx/… or https://doi.org/…), PMID, PMCID (e.g. PMC1234567), or repository URL." - Network accessline 348
ftp_base = ( f"https://ftp.ncbi.nlm.nih.gov/geo/series/" - Network accessline 348
ftp_base = ( f"https://ftp.ncbi.nlm.nih.gov/geo/series/" - Network accessline 349
f"https://ftp.ncbi.nlm.nih.gov/geo/series/" - Network accessline 349
f"https://ftp.ncbi.nlm.nih.gov/geo/series/" - Network accessline 353
geo_descriptions: dict[str, str] = {} try: series_url = f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession}&targ=self&form=text&view=quick" - Network accessline 353
geo_descriptions: dict[str, str] = {} try: series_url = f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession}&targ=self&form=text&view=quick" - Network accessline 354
try: series_url = f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession}&targ=self&form=text&view=quick" sr = requests.get(series_url, timeout=10) - Network accessline 354
try: series_url = f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession}&targ=self&form=text&view=quick" sr = requests.get(series_url, timeout=10) - Network accessline 355
series_url = f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession}&targ=self&form=text&view=quick" sr = requests.get(series_url, timeout=10) if sr.status_code == 200: - Network accessline 355
series_url = f"https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession}&targ=self&form=text&view=quick" sr = requests.get(series_url, timeout=10) if sr.status_code == 200: - Network accessline 356
sr = requests.get(series_url, timeout=10) - Network accessline 356
sr = requests.get(series_url, timeout=10) - Network accessline 367
try: r = requests.get(ftp_base, timeout=10) - Network accessline 367
try: r = requests.get(ftp_base, timeout=10) - Network accessline 368
r = requests.get(ftp_base, timeout=10) - Network accessline 368
r = requests.get(ftp_base, timeout=10) - Network accessline 450
} try: r = requests.get(ENA_PORTAL, params=params, timeout=15) - Network accessline 450
} try: r = requests.get(ENA_PORTAL, params=params, timeout=15) - Network accessline 451
try: r = requests.get(ENA_PORTAL, params=params, timeout=15) if r.status_code == 200: - Network accessline 451
try: r = requests.get(ENA_PORTAL, params=params, timeout=15) if r.status_code == 200: - Network accessline 452
r = requests.get(ENA_PORTAL, params=params, timeout=15) - Network accessline 452
r = requests.get(ENA_PORTAL, params=params, timeout=15) - Network accessline 477
try: r = requests.get(f"{ZENODO_BASE}/{record_id}", timeout=10) - Network accessline 477
try: r = requests.get(f"{ZENODO_BASE}/{record_id}", timeout=10) - Network accessline 478
r = requests.get(f"{ZENODO_BASE}/{record_id}", timeout=10) - Network accessline 478
r = requests.get(f"{ZENODO_BASE}/{record_id}", timeout=10) - Network accessline 503
files: list[dict] = [] try: url = f"https://zenodo.org/api/communities/{slug}/records" - Network accessline 503
files: list[dict] = [] try: url = f"https://zenodo.org/api/communities/{slug}/records" - Network accessline 504
try: url = f"https://zenodo.org/api/communities/{slug}/records" r = requests.get(url, params={"size": 25}, timeout=15) - Network accessline 504
try: url = f"https://zenodo.org/api/communities/{slug}/records" r = requests.get(url, params={"size": 25}, timeout=15) - Network accessline 505
url = f"https://zenodo.org/api/communities/{slug}/records" r = requests.get(url, params={"size": 25}, timeout=15) if r.status_code == 200: - Network accessline 505
url = f"https://zenodo.org/api/communities/{slug}/records" r = requests.get(url, params={"size": 25}, timeout=15) if r.status_code == 200: - Network accessline 506
r = requests.get(url, params={"size": 25}, timeout=15) - Network accessline 506
r = requests.get(url, params={"size": 25}, timeout=15) - Network accessline 541
try: print(f" 🔎 Zenodo: {query}") r = requests.get( - Network accessline 541
try: print(f" 🔎 Zenodo: {query}") r = requests.get( - Network accessline 542
print(f" 🔎 Zenodo: {query}") r = requests.get( "https://zenodo.org/api/records", - Network accessline 542
print(f" 🔎 Zenodo: {query}") r = requests.get( "https://zenodo.org/api/records", - Network accessline 543
r = requests.get( - Network accessline 543
r = requests.get( - Network accessline 544
"https://zenodo.org/api/records", - Network accessline 544
"https://zenodo.org/api/records", - Network accessline 592
try: print(f" 🔎 GEO: {term}") r = requests.get( - Network accessline 592
try: print(f" 🔎 GEO: {term}") r = requests.get( - Network accessline 593
print(f" 🔎 GEO: {term}") r = requests.get( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi", - Network accessline 593
print(f" 🔎 GEO: {term}") r = requests.get( "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi", - Network accessline 594
r = requests.get( - Network accessline 594
r = requests.get( - Network accessline 595
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi", - Network accessline 595
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi", - Network accessline 605
sr = requests.get( - Network accessline 605
sr = requests.get( - Network accessline 606
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi", - Network accessline 606
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi", - Network accessline 635
try: print(f" 🔎 ENA: {field}={value}") r = requests.get( - Network accessline 635
try: print(f" 🔎 ENA: {field}={value}") r = requests.get( - Network accessline 636
print(f" 🔎 ENA: {field}={value}") r = requests.get( "https://www.ebi.ac.uk/ena/portal/api/search", - Network accessline 636
print(f" 🔎 ENA: {field}={value}") r = requests.get( "https://www.ebi.ac.uk/ena/portal/api/search", - Network accessline 637
r = requests.get( - Network accessline 637
r = requests.get( - Network accessline 638
"https://www.ebi.ac.uk/ena/portal/api/search", - Network accessline 638
"https://www.ebi.ac.uk/ena/portal/api/search", - Network accessline 667
try: print(f" 🔎 Dryad: {doi}") r = requests.get( - Network accessline 667
try: print(f" 🔎 Dryad: {doi}") r = requests.get( - Network accessline 668
print(f" 🔎 Dryad: {doi}") r = requests.get( "https://datadryad.org/api/v2/search", - Network accessline 668
print(f" 🔎 Dryad: {doi}") r = requests.get( "https://datadryad.org/api/v2/search", - Network accessline 669
r = requests.get( - Network accessline 669
r = requests.get( - Network accessline 670
"https://datadryad.org/api/v2/search", - Network accessline 670
"https://datadryad.org/api/v2/search", - Network accessline 681
print(f" • {title[:70]}") if download_uri: url = f"https://datadryad.org{download_uri}" if download_uri.startswith("/") else download_uri - Network accessline 681
print(f" • {title[:70]}") if download_uri: url = f"https://datadryad.org{download_uri}" if download_uri.startswith("/") else download_uri - Network accessline 682
if download_uri: url = f"https://datadryad.org{download_uri}" if download_uri.startswith("/") else download_uri files.append({ - Network accessline 682
if download_uri: url = f"https://datadryad.org{download_uri}" if download_uri.startswith("/") else download_uri files.append({ - Network accessline 683
url = f"https://datadryad.org{download_uri}" if download_uri.startswith("/") else download_uri - Network accessline 683
url = f"https://datadryad.org{download_uri}" if download_uri.startswith("/") else download_uri - Network accessline 704
try: print(f" 🔎 DataCite (meta-index): {doi}") r = requests.get( - Network accessline 704
try: print(f" 🔎 DataCite (meta-index): {doi}") r = requests.get( - Network accessline 705
print(f" 🔎 DataCite (meta-index): {doi}") r = requests.get( "https://api.datacite.org/dois", - Network accessline 705
print(f" 🔎 DataCite (meta-index): {doi}") r = requests.get( "https://api.datacite.org/dois", - Network accessline 706
r = requests.get( - Network accessline 706
r = requests.get( - Network accessline 707
"https://api.datacite.org/dois", - Network accessline 707
"https://api.datacite.org/dois", - Network accessline 793
try: r = requests.get(url, stream=True, timeout=30) - Network accessline 793
try: r = requests.get(url, stream=True, timeout=30) - Network accessline 794
r = requests.get(url, stream=True, timeout=30) - Network accessline 794
r = requests.get(url, stream=True, timeout=30)
skills/article-data-fetcher/tests/test_article_data_fetcher.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 40
def test_url(self): kind, value = parse_identifier("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456") - Network accessline 40
def test_url(self): kind, value = parse_identifier("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456") - Network accessline 41
kind, value = parse_identifier("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456") - Network accessline 41
kind, value = parse_identifier("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123456")
skills/bgpt-mcp/SKILL.md
- Network accessline 43
python: '>=3.10' endpoints: mcp_sse: https://bgpt.pro/mcp/sse - Network accessline 43
python: '>=3.10' endpoints: mcp_sse: https://bgpt.pro/mcp/sse - Network accessline 44
endpoints: mcp_sse: https://bgpt.pro/mcp/sse mcp_stream: https://bgpt.pro/mcp/stream - Network accessline 44
endpoints: mcp_sse: https://bgpt.pro/mcp/sse mcp_stream: https://bgpt.pro/mcp/stream - Network accessline 45
mcp_sse: https://bgpt.pro/mcp/sse - Network accessline 45
mcp_sse: https://bgpt.pro/mcp/sse - Network accessline 46
mcp_stream: https://bgpt.pro/mcp/stream - Network accessline 46
mcp_stream: https://bgpt.pro/mcp/stream - Network accessline 48
always: false emoji: 🔬 homepage: https://bgpt.pro/mcp - Network accessline 48
always: false emoji: 🔬 homepage: https://bgpt.pro/mcp - Network accessline 49
emoji: 🔬 homepage: https://bgpt.pro/mcp os: - Network accessline 49
emoji: 🔬 homepage: https://bgpt.pro/mcp os: - Network accessline 50
homepage: https://bgpt.pro/mcp - Network accessline 50
homepage: https://bgpt.pro/mcp - Network accessline 125
1. **Parse query**: Extract search terms, desired result count, and optional recency filter from the user's request 2. **Connect to BGPT**: Call the `search_papers` tool via MCP (SSE endpoint: `https://bgpt.pro/mcp/sse`) - Network accessline 125
1. **Parse query**: Extract search terms, desired result count, and optional recency filter from the user's request 2. **Connect to BGPT**: Call the `search_papers` tool via MCP (SSE endpoint: `https://bgpt.pro/mcp/sse`) - Network accessline 126
2. **Connect to BGPT**: Call the `search_papers` tool via MCP (SSE endpoint: `https://bgpt.pro/mcp/sse`) - Network accessline 126
2. **Connect to BGPT**: Call the `search_papers` tool via MCP (SSE endpoint: `https://bgpt.pro/mcp/sse`) - Network accessline 140
SSE endpoint: https://bgpt.pro/mcp/sse - Network accessline 140
SSE endpoint: https://bgpt.pro/mcp/sse - Network accessline 141
Streamable HTTP endpoint: https://bgpt.pro/mcp/stream - Network accessline 141
Streamable HTTP endpoint: https://bgpt.pro/mcp/stream - Network accessline 148
"mcpServers": { "bgpt": { "url": "https://bgpt.pro/mcp/sse" - Network accessline 148
"mcpServers": { "bgpt": { "url": "https://bgpt.pro/mcp/sse" - Network accessline 149
"bgpt": { "url": "https://bgpt.pro/mcp/sse" } - Network accessline 149
"bgpt": { "url": "https://bgpt.pro/mcp/sse" } - Network accessline 150
"url": "https://bgpt.pro/mcp/sse" - Network accessline 150
"url": "https://bgpt.pro/mcp/sse" - Access to secretsline 163
[Credential-related source omitted] - Access to secretsline 163
[Credential-related source omitted] - Network accessline 334
|------|------|---------| | Free | $0 | 50 free results, no API key needed | | Pay-as-you-go | $0.01/result | Get an API key at [bgpt.pro/mcp](https://bgpt.pro/mcp) | - Network accessline 334
|------|------|---------| | Free | $0 | 50 free results, no API key needed | | Pay-as-you-go | $0.01/result | Get an API key at [bgpt.pro/mcp](https://bgpt.pro/mcp) | - Network accessline 336
| Pay-as-you-go | $0.01/result | Get an API key at [bgpt.pro/mcp](https://bgpt.pro/mcp) | - Network accessline 336
| Pay-as-you-go | $0.01/result | Get an API key at [bgpt.pro/mcp](https://bgpt.pro/mcp) | - Network accessline 340
- [BGPT MCP Server](https://bgpt.pro/mcp); full-text paper data extraction and search API - Network accessline 340
- [BGPT MCP Server](https://bgpt.pro/mcp); full-text paper data extraction and search API - Network accessline 341
- [Model Context Protocol](https://modelcontextprotocol.io/); open protocol for AI tool integration - Network accessline 341
- [Model Context Protocol](https://modelcontextprotocol.io/); open protocol for AI tool integration - Network accessline 342
- [bgpt-mcp on GitHub](https://github.com/connerlambden/bgpt-mcp); source repository and documentation - Network accessline 342
- [bgpt-mcp on GitHub](https://github.com/connerlambden/bgpt-mcp); source repository and documentation - Network accessline 343
- [bgpt-mcp on npm](https://www.npmjs.com/package/bgpt-mcp); npm package for local MCP proxy - Network accessline 343
- [bgpt-mcp on npm](https://www.npmjs.com/package/bgpt-mcp); npm package for local MCP proxy
skills/bgpt-mcp/tests/test_bgpt_mcp.py
skills/bigquery-public/SKILL.md
- Network accessline 19
always: false emoji: 🗃<U+FE0F> homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
always: false emoji: 🗃<U+FE0F> homepage: https://github.com/ClawBio/ClawBio - Network accessline 20
emoji: 🗃<U+FE0F> homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 20
emoji: 🗃<U+FE0F> homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 21
homepage: https://github.com/ClawBio/ClawBio - Network accessline 21
homepage: https://github.com/ClawBio/ClawBio - Network accessline 177
- [BigQuery public datasets](https://cloud.google.com/bigquery/public-data) - Network accessline 177
- [BigQuery public datasets](https://cloud.google.com/bigquery/public-data) - Network accessline 178
- [BigQuery authentication](https://cloud.google.com/bigquery/docs/authentication) - Network accessline 178
- [BigQuery authentication](https://cloud.google.com/bigquery/docs/authentication)
skills/bigquery-public/bigquery_backends.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 118
try: credentials, default_project = google.auth.default( scopes=["https://www.googleapis.com/auth/cloud-platform"] - Network accessline 118
try: credentials, default_project = google.auth.default( scopes=["https://www.googleapis.com/auth/cloud-platform"] - Network accessline 119
credentials, default_project = google.auth.default( scopes=["https://www.googleapis.com/auth/cloud-platform"] ) - Network accessline 119
credentials, default_project = google.auth.default( scopes=["https://www.googleapis.com/auth/cloud-platform"] ) - Network accessline 120
scopes=["https://www.googleapis.com/auth/cloud-platform"] - Network accessline 120
scopes=["https://www.googleapis.com/auth/cloud-platform"]
skills/bigquery-public/bigquery_models.py
skills/bigquery-public/bigquery_public.py
skills/bigquery-public/bigquery_support.py
skills/bigquery-public/tests/test_bigquery_public.py
skills/bio-orchestrator/SKILL.md
- Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio
skills/bio-orchestrator/orchestrator.py
skills/bio-orchestrator/tests/test_orchestrator.py
skills/bio-orchestrator/tests/test_skill_intents.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 480
[Credential-related source omitted] - Access to secretsline 480
[Credential-related source omitted] - Access to secretsline 516
[Credential-related source omitted] - Access to secretsline 516
[Credential-related source omitted]
skills/bioconductor-bridge/SKILL.md
- Network accessline 23
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 24
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 222
- [Bioconductor](https://www.bioconductor.org/) — official project and package ecosystem - Network accessline 222
- [Bioconductor](https://www.bioconductor.org/) — official project and package ecosystem - Network accessline 223
- [BiocManager](https://bioconductor.org/install/) — official installation and version-management guidance - Network accessline 223
- [BiocManager](https://bioconductor.org/install/) — official installation and version-management guidance - Network accessline 224
- [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) — canonical assay container - Network accessline 224
- [SummarizedExperiment](https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html) — canonical assay container - Network accessline 225
- [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) — canonical single-cell container - Network accessline 225
- [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) — canonical single-cell container - Network accessline 226
- [GenomicRanges](https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html) — canonical interval container - Network accessline 226
- [GenomicRanges](https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html) — canonical interval container - Network accessline 227
- [VariantAnnotation](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) — canonical VCF and variant annotation package - Network accessline 227
- [VariantAnnotation](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) — canonical VCF and variant annotation package
skills/bioconductor-bridge/bioc_recommender.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 407
[Credential-related source omitted] - Access to secretsline 407
[Credential-related source omitted] - Network accessline 463
def _official_url(name: str) -> str: return f"https://bioconductor.org/packages/{name}/" - Network accessline 463
def _official_url(name: str) -> str: return f"https://bioconductor.org/packages/{name}/" - Network accessline 464
return f"https://bioconductor.org/packages/{name}/" - Network accessline 464
return f"https://bioconductor.org/packages/{name}/"
skills/bioconductor-bridge/bioconductor_bridge.py
skills/bioconductor-bridge/tests/test_bioc_recommender.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 21
"version": "1.0.0", "biocViews": ["Infrastructure", "Transcriptomics"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 21
"version": "1.0.0", "biocViews": ["Infrastructure", "Transcriptomics"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 22
"biocViews": ["Infrastructure", "Transcriptomics"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", "repo_name": "BioCsoft", - Network accessline 22
"biocViews": ["Infrastructure", "Transcriptomics"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", "repo_name": "BioCsoft", - Network accessline 23
"repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 23
"repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 24
"repo_name": "BioCsoft", "official_url": "https://bioconductor.org/packages/SummarizedExperiment/", "domains": ["bulk_rnaseq"], - Network accessline 24
"repo_name": "BioCsoft", "official_url": "https://bioconductor.org/packages/SummarizedExperiment/", "domains": ["bulk_rnaseq"], - Network accessline 25
"official_url": "https://bioconductor.org/packages/SummarizedExperiment/", - Network accessline 25
"official_url": "https://bioconductor.org/packages/SummarizedExperiment/", - Network accessline 38
"version": "1.0.0", "biocViews": ["RNASeq", "DifferentialExpression"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 38
"version": "1.0.0", "biocViews": ["RNASeq", "DifferentialExpression"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 39
"biocViews": ["RNASeq", "DifferentialExpression"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", "repo_name": "BioCsoft", - Network accessline 39
"biocViews": ["RNASeq", "DifferentialExpression"], "repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", "repo_name": "BioCsoft", - Network accessline 40
"repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 40
"repository": "https://bioconductor.org/packages/3.23/bioc/src/contrib", - Network accessline 41
"repo_name": "BioCsoft", "official_url": "https://bioconductor.org/packages/DESeq2/", "domains": ["bulk_rnaseq"], - Network accessline 41
"repo_name": "BioCsoft", "official_url": "https://bioconductor.org/packages/DESeq2/", "domains": ["bulk_rnaseq"], - Network accessline 42
"official_url": "https://bioconductor.org/packages/DESeq2/", - Network accessline 42
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Executable file - Executable scriptline 1
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"official_url": "https://bioconductor.org/packages/ATACseqQC/", - Access to secretsline 324
[Credential-related source omitted] - Access to secretsline 324
[Credential-related source omitted] - Access to secretsline 349
[Credential-related source omitted] - Access to secretsline 349
[Credential-related source omitted]
skills/bioqc-mcp/SKILL.md
- Network accessline 44
always: false emoji: 📊 homepage: https://github.com/Babajan-B/BioQC-MCP - Network accessline 44
always: false emoji: 📊 homepage: https://github.com/Babajan-B/BioQC-MCP - Network accessline 45
emoji: 📊 homepage: https://github.com/Babajan-B/BioQC-MCP os: - Network accessline 45
emoji: 📊 homepage: https://github.com/Babajan-B/BioQC-MCP os: - Network accessline 46
homepage: https://github.com/Babajan-B/BioQC-MCP - Network accessline 46
homepage: https://github.com/Babajan-B/BioQC-MCP - Network accessline 208
- Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data (2010). http://www.bioinformatics.babraham.ac.uk/projects/fastqc - Network accessline 208
- Andrews S. FastQC: A Quality Control Tool for High Throughput Sequence Data (2010). http://www.bioinformatics.babraham.ac.uk/projects/fastqc
skills/bioqc-mcp/bioqc_mcp.py
skills/bioqc-mcp/tests/test_bioqc_mcp.py
skills/biostudies-fetch/SKILL.md
- Network accessline 65
always: false emoji: "🗂<U+FE0F>" homepage: https://www.ebi.ac.uk/biostudies/ - Network accessline 65
always: false emoji: "🗂<U+FE0F>" homepage: https://www.ebi.ac.uk/biostudies/ - Network accessline 66
emoji: "🗂<U+FE0F>" homepage: https://www.ebi.ac.uk/biostudies/ os: - Network accessline 66
emoji: "🗂<U+FE0F>" homepage: https://www.ebi.ac.uk/biostudies/ os: - Network accessline 67
homepage: https://www.ebi.ac.uk/biostudies/ - Network accessline 67
homepage: https://www.ebi.ac.uk/biostudies/ - Network accessline 204
1. **Fetch**: `GET https://www.ebi.ac.uk/biostudies/api/v1/studies/{accession}`, - Network accessline 204
1. **Fetch**: `GET https://www.ebi.ac.uk/biostudies/api/v1/studies/{accession}`, - Network accessline 238
Source: [EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/S-BSST2074) - Network accessline 238
Source: [EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/S-BSST2074) - Network accessline 308
a thin result. - **Gotcha 5**: You will want to hardcode the classic `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}` download URL. Do - Network accessline 308
a thin result. - **Gotcha 5**: You will want to hardcode the classic `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}` download URL. Do - Network accessline 309
- **Gotcha 5**: You will want to hardcode the classic `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}` download URL. Do not. It works — it 302-redirects — but there is no one base tree behind it: - Network accessline 309
- **Gotcha 5**: You will want to hardcode the classic `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}` download URL. Do not. It works — it 302-redirects — but there is no one base tree behind it: - Network accessline 310
`https://www.ebi.ac.uk/biostudies/files/{accession}/{path}` download URL. Do - Network accessline 310
`https://www.ebi.ac.uk/biostudies/files/{accession}/{path}` download URL. Do - Network accessline 324
"open FTP" will not help. Confirm with `curl -sI https://ftp.ebi.ac.uk/biostudies/ -o /dev/null -w '%{http_code}\n'`: - Network accessline 324
"open FTP" will not help. Confirm with `curl -sI https://ftp.ebi.ac.uk/biostudies/ -o /dev/null -w '%{http_code}\n'`: - Network accessline 325
Confirm with `curl -sI https://ftp.ebi.ac.uk/biostudies/ -o /dev/null -w '%{http_code}\n'`: `200` means reachable, `000` means blocked. - Network accessline 325
Confirm with `curl -sI https://ftp.ebi.ac.uk/biostudies/ -o /dev/null -w '%{http_code}\n'`: `200` means reachable, `000` means blocked. - Network accessline 326
`curl -sI https://ftp.ebi.ac.uk/biostudies/ -o /dev/null -w '%{http_code}\n'`: - Network accessline 326
`curl -sI https://ftp.ebi.ac.uk/biostudies/ -o /dev/null -w '%{http_code}\n'`: - Network accessline 393
- [EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/); the archive and its - Network accessline 393
- [EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/); the archive and its - Network accessline 394
REST API. - [EBI BioSamples](https://www.ebi.ac.uk/biosamples/); sample characteristics used to enrich the metadata table. - Network accessline 394
REST API. - [EBI BioSamples](https://www.ebi.ac.uk/biosamples/); sample characteristics used to enrich the metadata table. - Network accessline 395
- [EBI BioSamples](https://www.ebi.ac.uk/biosamples/); sample characteristics - Network accessline 395
- [EBI BioSamples](https://www.ebi.ac.uk/biosamples/); sample characteristics - Network accessline 396
used to enrich the metadata table. - Demo fixture: [S-BSST2074](https://www.ebi.ac.uk/biostudies/studies/S-BSST2074), doi:10.6019/S-BSST2074, licensed CC0. - Network accessline 396
used to enrich the metadata table. - Demo fixture: [S-BSST2074](https://www.ebi.ac.uk/biostudies/studies/S-BSST2074), doi:10.6019/S-BSST2074, licensed CC0. - Network accessline 397
- Demo fixture: [S-BSST2074](https://www.ebi.ac.uk/biostudies/studies/S-BSST2074), - Network accessline 397
- Demo fixture: [S-BSST2074](https://www.ebi.ac.uk/biostudies/studies/S-BSST2074), - Network accessline 398
doi:10.6019/S-BSST2074, licensed CC0. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 398
doi:10.6019/S-BSST2074, licensed CC0. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 399
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`biostudies/`), © 2026 UK Dementia Research Institute, MIT. - Network accessline 399
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`biostudies/`), © 2026 UK Dementia Research Institute, MIT. - Network accessline 400
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 400
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills)
skills/biostudies-fetch/biostudies_fetch.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 134
output_dir, title=f"BioStudies report — {accession}", source_url=f"[EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/{accession})", - Network accessline 134
output_dir, title=f"BioStudies report — {accession}", source_url=f"[EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/{accession})", - Network accessline 135
title=f"BioStudies report — {accession}", source_url=f"[EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/{accession})", sections=sections, - Network accessline 135
title=f"BioStudies report — {accession}", source_url=f"[EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/{accession})", sections=sections, - Network accessline 136
source_url=f"[EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/{accession})", - Network accessline 136
source_url=f"[EMBL-EBI BioStudies](https://www.ebi.ac.uk/biostudies/studies/{accession})",
skills/biostudies-fetch/biostudies_fetch_api.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Uses the BioStudies REST API (https://www.ebi.ac.uk/biostudies/api/v1). Files are - Network accessline 8
Uses the BioStudies REST API (https://www.ebi.ac.uk/biostudies/api/v1). Files are - Network accessline 32
API = "https://www.ebi.ac.uk/biostudies/api/v1" - Network accessline 32
API = "https://www.ebi.ac.uk/biostudies/api/v1" - Network accessline 33
FILES = "https://www.ebi.ac.uk/biostudies/files" - Network accessline 33
FILES = "https://www.ebi.ac.uk/biostudies/files" - Network accessline 39
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 39
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 40
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 40
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 41
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 41
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 42
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 42
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 130
DIVERGES FROM UPSTREAM, deliberately. Upstream hardcodes `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. That route is - Network accessline 130
DIVERGES FROM UPSTREAM, deliberately. Upstream hardcodes `https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. That route is - Network accessline 131
`https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. That route is - Network accessline 131
`https://www.ebi.ac.uk/biostudies/files/{accession}/{path}`. That route is - Network accessline 169
return dest print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 169
return dest print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 170
print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 170
print(f" downloading {path} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 171
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 171
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 172
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 172
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 331
try: data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 331
try: data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 332
data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) .decode("utf-8", "replace")) - Network accessline 332
data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) .decode("utf-8", "replace")) - Network accessline 333
http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 333
http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession)
skills/biostudies-fetch/examples/demo_S-BSST2074.json
- Network accessline 32
{ "name": "Description", "value": "The aim was to analyze scRNAseq data from four distinct mouse species: Mus musculus strains C57BL/6J and Ly5.1, (BL6), Mus musculus castaneus, Mus spretus, and Mus caroli. W - Network accessline 32
{ "name": "Description", "value": "The aim was to analyze scRNAseq data from four distinct mouse species: Mus musculus strains C57BL/6J and Ly5.1, (BL6), Mus musculus castaneus, Mus spretus, and Mus caroli. W - Network accessline 33
"name": "Description", "value": "The aim was to analyze scRNAseq data from four distinct mouse species: Mus musculus strains C57BL/6J and Ly5.1, (BL6), Mus musculus castaneus, Mus spretus, and Mus caroli. We generated a 10X - Network accessline 33
"name": "Description", "value": "The aim was to analyze scRNAseq data from four distinct mouse species: Mus musculus strains C57BL/6J and Ly5.1, (BL6), Mus musculus castaneus, Mus spretus, and Mus caroli. We generated a 10X - Network accessline 34
"value": "The aim was to analyze scRNAseq data from four distinct mouse species: Mus musculus strains C57BL/6J and Ly5.1, (BL6), Mus musculus castaneus, Mus spretus, and Mus caroli. We generated a 10X Genomics Cell Ranger (Zheng et al. 2017 - Network accessline 34
"value": "The aim was to analyze scRNAseq data from four distinct mouse species: Mus musculus strains C57BL/6J and Ly5.1, (BL6), Mus musculus castaneus, Mus spretus, and Mus caroli. We generated a 10X Genomics Cell Ranger (Zheng et al. 2017 - Network accessline 56
{ "name": "URL", "value": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" - Network accessline 56
{ "name": "URL", "value": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" - Network accessline 57
"name": "URL", "value": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" } - Network accessline 57
"name": "URL", "value": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" } - Network accessline 58
"value": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" - Network accessline 58
"value": "https://creativecommons.org/publicdomain/zero/1.0/legalcode" - Network accessline 76
"links": [ { "url": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15073" - Network accessline 76
"links": [ { "url": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15073" - Network accessline 77
{ "url": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15073" } - Network accessline 77
{ "url": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15073" } - Network accessline 78
"url": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15073" - Network accessline 78
"url": "https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-15073"
skills/biostudies-fetch/examples/demo_search.json
skills/biostudies-fetch/tests/test_biostudies_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 364
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074", - Network accessline 364
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074", - Network accessline 367
url = api.file_url("S-BSST2074", "GRCm38_masked_allStrains.zip") assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074" - Network accessline 367
url = api.file_url("S-BSST2074", "GRCm38_masked_allStrains.zip") assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074" - Network accessline 368
assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074" "/Files/GRCm38_masked_allStrains.zip") - Network accessline 368
assert url == ( "https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074" "/Files/GRCm38_masked_allStrains.zip") - Network accessline 369
"https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074" - Network accessline 369
"https://ftp.ebi.ac.uk/biostudies/fire/S-BSST/074/S-BSST2074" - Network accessline 375
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/S-B/001/S-B1"} - Network accessline 375
info = {"httpLink": "https://ftp.ebi.ac.uk/biostudies/fire/S-B/001/S-B1"} - Network accessline 383
with patch.object(api, "get_json", return_value={}): assert api.file_url("S-B1", "b.txt") == \ "https://www.ebi.ac.uk/biostudies/files/S-B1/b.txt" - Network accessline 383
with patch.object(api, "get_json", return_value={}): assert api.file_url("S-B1", "b.txt") == \ "https://www.ebi.ac.uk/biostudies/files/S-B1/b.txt" - Network accessline 384
assert api.file_url("S-B1", "b.txt") == "https://www.ebi.ac.uk/biostudies/files/S-B1/b.txt" - Network accessline 384
assert api.file_url("S-B1", "b.txt") == "https://www.ebi.ac.uk/biostudies/files/S-B1/b.txt" - Network accessline 385
"https://www.ebi.ac.uk/biostudies/files/S-B1/b.txt" - Network accessline 385
"https://www.ebi.ac.uk/biostudies/files/S-B1/b.txt" - Network accessline 387
@pytest.mark.parametrize("link", [ "https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 387
@pytest.mark.parametrize("link", [ "https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 388
"https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 388
"https://evil.example/x", "https://ebi.ac.uk.evil.com/x", - Network accessline 389
"http://ftp.ebi.ac.uk/x", "file:///etc", - Network accessline 389
"http://ftp.ebi.ac.uk/x", "file:///etc",
skills/busco-assessor/SKILL.md
- Network accessline 65
always: false emoji: "🧬" homepage: https://busco.ezlab.org/ - Network accessline 65
always: false emoji: "🧬" homepage: https://busco.ezlab.org/ - Network accessline 66
emoji: "🧬" homepage: https://busco.ezlab.org/ os: - Network accessline 66
emoji: "🧬" homepage: https://busco.ezlab.org/ os: - Network accessline 67
homepage: https://busco.ezlab.org/ - Network accessline 67
homepage: https://busco.ezlab.org/ - Network accessline 229
esearch → https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term={name}&retmode=json - Network accessline 229
esearch → https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term={name}&retmode=json - Network accessline 232
efetch → https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=4932&retmode=xml - Network accessline 232
efetch → https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&id=4932&retmode=xml - Network accessline 409
- Manni M. et al. (2021). BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage. *Molecular Biology and Evolution*. https://doi.org/10.1093/molbev/msab199 - Network accessline 409
- Manni M. et al. (2021). BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage. *Molecular Biology and Evolution*. https://doi.org/10.1093/molbev/msab199 - Network accessline 410
- Simão F.A. et al. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. *Bioinformatics*. https://doi.org/10.1093/bioinformatics/btv351 - Network accessline 410
- Simão F.A. et al. (2015). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. *Bioinformatics*. https://doi.org/10.1093/bioinformatics/btv351 - Network accessline 411
- OrthoDB v10/v12: https://www.orthodb.org/ - Network accessline 411
- OrthoDB v10/v12: https://www.orthodb.org/ - Network accessline 412
- BUSCO GitLab: https://gitlab.com/ezlab/busco - Network accessline 412
- BUSCO GitLab: https://gitlab.com/ezlab/busco - Network accessline 413
- BUSCO User Guide v6: https://busco.ezlab.org/busco_userguide.html - Network accessline 413
- BUSCO User Guide v6: https://busco.ezlab.org/busco_userguide.html
skills/busco-assessor/busco_assessor.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 127
NCBI_EUTILS_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Network accessline 127
NCBI_EUTILS_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 133
[Credential-related source omitted] - Access to secretsline 133
[Credential-related source omitted] - Network accessline 138
DEMO_LIVE_URL = ( "https://ftp.ensemblgenomes.org/pub/fungi/release-62/fasta/" - Network accessline 138
DEMO_LIVE_URL = ( "https://ftp.ensemblgenomes.org/pub/fungi/release-62/fasta/" - Network accessline 139
"https://ftp.ensemblgenomes.org/pub/fungi/release-62/fasta/" - Network accessline 139
"https://ftp.ensemblgenomes.org/pub/fungi/release-62/fasta/" - Access to secretsline 747
[Credential-related source omitted] - Access to secretsline 747
[Credential-related source omitted] - Network accessline 750
f"?db=taxonomy&term={query}&retmode=json{key_param}" ) search_req = urllib.request.Request( - Network accessline 750
f"?db=taxonomy&term={query}&retmode=json{key_param}" ) search_req = urllib.request.Request( - Network accessline 751
) search_req = urllib.request.Request( search_url, headers={"User-Agent": NCBI_USER_AGENT} - Network accessline 751
) search_req = urllib.request.Request( search_url, headers={"User-Agent": NCBI_USER_AGENT} - Network accessline 752
search_req = urllib.request.Request( - Network accessline 752
search_req = urllib.request.Request( - Network accessline 753
search_url, headers={"User-Agent": NCBI_USER_AGENT} ) with urllib.request.urlopen(search_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 753
search_url, headers={"User-Agent": NCBI_USER_AGENT} ) with urllib.request.urlopen(search_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 754
) with urllib.request.urlopen(search_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: data = json.loads(resp.read()) - Network accessline 754
) with urllib.request.urlopen(search_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: data = json.loads(resp.read()) - Network accessline 755
with urllib.request.urlopen(search_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 755
with urllib.request.urlopen(search_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 765
f"?db=taxonomy&id={taxid}&retmode=xml{key_param}" ) fetch_req = urllib.request.Request( - Network accessline 765
f"?db=taxonomy&id={taxid}&retmode=xml{key_param}" ) fetch_req = urllib.request.Request( - Network accessline 766
) fetch_req = urllib.request.Request( fetch_url, headers={"User-Agent": NCBI_USER_AGENT} - Network accessline 766
) fetch_req = urllib.request.Request( fetch_url, headers={"User-Agent": NCBI_USER_AGENT} - Network accessline 767
fetch_req = urllib.request.Request( - Network accessline 767
fetch_req = urllib.request.Request( - Network accessline 768
fetch_url, headers={"User-Agent": NCBI_USER_AGENT} ) with urllib.request.urlopen(fetch_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 768
fetch_url, headers={"User-Agent": NCBI_USER_AGENT} ) with urllib.request.urlopen(fetch_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 769
) with urllib.request.urlopen(fetch_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: xml_bytes = resp.read() - Network accessline 769
) with urllib.request.urlopen(fetch_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: xml_bytes = resp.read() - Network accessline 770
with urllib.request.urlopen(fetch_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 770
with urllib.request.urlopen(fetch_req, timeout=NCBI_REQUEST_TIMEOUT) as resp: - Network accessline 825
print(f" Downloading {filename} ({url}) ...") total = 0 with urllib.request.urlopen(url, timeout=NCBI_REQUEST_TIMEOUT) as resp, \ - Network accessline 825
print(f" Downloading {filename} ({url}) ...") total = 0 with urllib.request.urlopen(url, timeout=NCBI_REQUEST_TIMEOUT) as resp, \ - Network accessline 826
total = 0 with urllib.request.urlopen(url, timeout=NCBI_REQUEST_TIMEOUT) as resp, \ open(gz_path, "wb") as fh: - Network accessline 826
total = 0 with urllib.request.urlopen(url, timeout=NCBI_REQUEST_TIMEOUT) as resp, \ open(gz_path, "wb") as fh: - Network accessline 827
with urllib.request.urlopen(url, timeout=NCBI_REQUEST_TIMEOUT) as resp, \ - Network accessline 827
with urllib.request.urlopen(url, timeout=NCBI_REQUEST_TIMEOUT) as resp, \
skills/busco-assessor/tests/__init__.py
skills/busco-assessor/tests/test_busco_assessor.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 388
<?xml version="1.0" ?> <!DOCTYPE TaxaSet PUBLIC "-//NLM//DTD Taxon, 14th January 2002//EN" "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd"> - Network accessline 388
<?xml version="1.0" ?> <!DOCTYPE TaxaSet PUBLIC "-//NLM//DTD Taxon, 14th January 2002//EN" "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd"> - Network accessline 389
<!DOCTYPE TaxaSet PUBLIC "-//NLM//DTD Taxon, 14th January 2002//EN" "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd"> <TaxaSet> - Network accessline 389
<!DOCTYPE TaxaSet PUBLIC "-//NLM//DTD Taxon, 14th January 2002//EN" "https://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd"> <TaxaSet> - Network accessline 390
"https://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd"> - Network accessline 390
"https://www.ncbi.nlm.nih.gov/entrez/query/DTD/taxon.dtd"> - Network accessline 484
def test_saccharomyces_lookup_returns_saccharomycetes(self): mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 484
def test_saccharomyces_lookup_returns_saccharomycetes(self): mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 485
mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): lineage = ncbi_taxonomy_lookup("Saccharomyces cerevisiae") - Network accessline 485
mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): lineage = ncbi_taxonomy_lookup("Saccharomyces cerevisiae") - Network accessline 486
with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 486
with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 491
def test_lookup_returns_rank_name_pairs(self): mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 491
def test_lookup_returns_rank_name_pairs(self): mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 492
mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): lineage = ncbi_taxonomy_lookup("Saccharomyces cerevisiae") - Network accessline 492
mock_urlopen = self._mock_urlopen(SEARCH_JSON, SACCHAROMYCES_XML.encode()) with patch("urllib.request.urlopen", mock_urlopen): lineage = ncbi_taxonomy_lookup("Saccharomyces cerevisiae") - Network accessline 493
with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 493
with patch("urllib.request.urlopen", mock_urlopen): - Network accessline 497
def test_network_error_returns_empty_list(self): import urllib.error with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 497
def test_network_error_returns_empty_list(self): import urllib.error with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 498
import urllib.error with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): lineage = ncbi_taxonomy_lookup("Saccharomyces cerevisiae") - Network accessline 498
import urllib.error with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): lineage = ncbi_taxonomy_lookup("Saccharomyces cerevisiae") - Network accessline 499
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 499
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 542
captured.append(req) raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen): - Network accessline 542
captured.append(req) raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen): - Network accessline 543
raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen): ncbi_taxonomy_lookup("anything") - Network accessline 543
raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen): ncbi_taxonomy_lookup("anything") - Network accessline 544
with patch("urllib.request.urlopen", side_effect=fake_urlopen): - Network accessline 544
with patch("urllib.request.urlopen", side_effect=fake_urlopen): - Network accessline 553
captured.append(req) raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ - Network accessline 553
captured.append(req) raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ - Network accessline 554
raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ patch("busco_assessor.NCBI_API_KEY", "testkey123"): - Network accessline 554
raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ patch("busco_assessor.NCBI_API_KEY", "testkey123"): - Network accessline 555
[Credential-related source omitted] - Network accessline 555
[Credential-related source omitted] - Access to secretsline 555
[Credential-related source omitted] - Access to secretsline 555
[Credential-related source omitted] - Access to secretsline 556
[Credential-related source omitted] - Access to secretsline 556
[Credential-related source omitted] - Access to secretsline 559
[Credential-related source omitted] - Access to secretsline 559
[Credential-related source omitted] - Network accessline 565
captured.append(req) raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ - Network accessline 565
captured.append(req) raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ - Network accessline 566
raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ patch("busco_assessor.NCBI_API_KEY", ""): - Network accessline 566
raise urllib.error.URLError("mock — short circuit") with patch("urllib.request.urlopen", side_effect=fake_urlopen), \ patch("busco_assessor.NCBI_API_KEY", ""): - Network accessline 567
[Credential-related source omitted] - Network accessline 567
[Credential-related source omitted] - Access to secretsline 567
[Credential-related source omitted] - Access to secretsline 567
[Credential-related source omitted] - Access to secretsline 568
[Credential-related source omitted] - Access to secretsline 568
[Credential-related source omitted] - Access to secretsline 571
[Credential-related source omitted] - Access to secretsline 571
[Credential-related source omitted] - Network accessline 615
def test_creates_decompressed_fasta(self, tmp_path): gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 615
def test_creates_decompressed_fasta(self, tmp_path): gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 616
gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): result = download_and_decompress( - Network accessline 616
gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): result = download_and_decompress( - Network accessline 617
with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 617
with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 618
result = download_and_decompress( "http://fake.example.com/test.fa.gz", tmp_path / "out" ) - Network accessline 618
result = download_and_decompress( "http://fake.example.com/test.fa.gz", tmp_path / "out" ) - Network accessline 619
"http://fake.example.com/test.fa.gz", tmp_path / "out" - Network accessline 619
"http://fake.example.com/test.fa.gz", tmp_path / "out" - Network accessline 625
def test_removes_gz_after_decompress(self, tmp_path): gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 625
def test_removes_gz_after_decompress(self, tmp_path): gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 626
gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): result = download_and_decompress( - Network accessline 626
gz_bytes = self._make_gz_bytes() with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): result = download_and_decompress( - Network accessline 627
with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 627
with patch("urllib.request.urlopen", self._mock_urlopen(gz_bytes)): - Network accessline 628
result = download_and_decompress( "http://fake.example.com/test.fa.gz", tmp_path / "out" ) - Network accessline 628
result = download_and_decompress( "http://fake.example.com/test.fa.gz", tmp_path / "out" ) - Network accessline 629
"http://fake.example.com/test.fa.gz", tmp_path / "out" - Network accessline 629
"http://fake.example.com/test.fa.gz", tmp_path / "out" - Network accessline 634
def test_raises_on_oversized_download(self, tmp_path): oversized = b"X" * (MAX_DOWNLOAD_BYTES + 1) with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 634
def test_raises_on_oversized_download(self, tmp_path): oversized = b"X" * (MAX_DOWNLOAD_BYTES + 1) with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 635
oversized = b"X" * (MAX_DOWNLOAD_BYTES + 1) with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ pytest.raises(RuntimeError, match="exceeded"): - Network accessline 635
oversized = b"X" * (MAX_DOWNLOAD_BYTES + 1) with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ pytest.raises(RuntimeError, match="exceeded"): - Network accessline 636
with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 636
with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 637
pytest.raises(RuntimeError, match="exceeded"): download_and_decompress( "http://fake.example.com/huge.fa.gz", tmp_path / "out" - Network accessline 637
pytest.raises(RuntimeError, match="exceeded"): download_and_decompress( "http://fake.example.com/huge.fa.gz", tmp_path / "out" - Network accessline 638
download_and_decompress( "http://fake.example.com/huge.fa.gz", tmp_path / "out" ) - Network accessline 638
download_and_decompress( "http://fake.example.com/huge.fa.gz", tmp_path / "out" ) - Network accessline 639
"http://fake.example.com/huge.fa.gz", tmp_path / "out" - Network accessline 639
"http://fake.example.com/huge.fa.gz", tmp_path / "out" - Network accessline 643
oversized = b"X" * (MAX_DOWNLOAD_BYTES + 1) out_dir = tmp_path / "out" with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 643
oversized = b"X" * (MAX_DOWNLOAD_BYTES + 1) out_dir = tmp_path / "out" with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 644
out_dir = tmp_path / "out" with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ pytest.raises(RuntimeError): - Network accessline 644
out_dir = tmp_path / "out" with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ pytest.raises(RuntimeError): - Network accessline 645
with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 645
with patch("urllib.request.urlopen", self._mock_urlopen(oversized)), \ - Network accessline 646
pytest.raises(RuntimeError): download_and_decompress("http://fake.example.com/huge.fa.gz", out_dir) leftover = list(out_dir.glob("*.gz")) if out_dir.exists() else [] - Network accessline 646
pytest.raises(RuntimeError): download_and_decompress("http://fake.example.com/huge.fa.gz", out_dir) leftover = list(out_dir.glob("*.gz")) if out_dir.exists() else [] - Network accessline 647
download_and_decompress("http://fake.example.com/huge.fa.gz", out_dir) - Network accessline 647
download_and_decompress("http://fake.example.com/huge.fa.gz", out_dir)
skills/cell-detection/SKILL.md
- Network accessline 21
always: false emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 21
always: false emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 22
emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 22
emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 23
homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
homepage: https://github.com/ClawBio/ClawBio - Network accessline 215
- [Pachitariu, Rariden & Stringer (2025) *Cellpose-SAM: superhuman generalization for cellular segmentation*. bioRxiv 2025.04.28.651001](https://doi.org/10.1101/2025.04.28.651001) — CellposeSAM / cpsam model - Network accessline 215
- [Pachitariu, Rariden & Stringer (2025) *Cellpose-SAM: superhuman generalization for cellular segmentation*. bioRxiv 2025.04.28.651001](https://doi.org/10.1101/2025.04.28.651001) — CellposeSAM / cpsam model
skills/cell-detection/cell_detection.py
skills/cell-detection/tests/test_cell_detection.py
skills/celltype-specificity-profiler/SKILL.md
- Network accessline 59
always: false emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio - Network accessline 59
always: false emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio - Network accessline 60
emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 60
emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 61
homepage: https://github.com/ClawBio/ClawBio - Network accessline 61
homepage: https://github.com/ClawBio/ClawBio
skills/celltype-specificity-profiler/profiler.py
skills/celltype-specificity-profiler/tests/test_profiler.py
skills/claw-amplicon-qc/SKILL.md
- Network accessline 117
category: bioinformatics emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 117
category: bioinformatics emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 118
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 118
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 119
homepage: https://github.com/ClawBio/ClawBio - Network accessline 119
homepage: https://github.com/ClawBio/ClawBio - Network accessline 493
- [DADA2](https://doi.org/10.1038/nmeth.3869) — Callahan et al. (2016), *Nature Methods* 13:581–583; single-nucleotide-resolution amplicon denoising, provides `filterAndTrim` used at Stage 2. - Network accessline 493
- [DADA2](https://doi.org/10.1038/nmeth.3869) — Callahan et al. (2016), *Nature Methods* 13:581–583; single-nucleotide-resolution amplicon denoising, provides `filterAndTrim` used at Stage 2. - Network accessline 494
- [Cutadapt](https://doi.org/10.14806/ej.17.1.200) — Martin (2011), *EMBnet.journal* 17(1):10–12; primer/adapter trimming, used at Stage 4. - Network accessline 494
- [Cutadapt](https://doi.org/10.14806/ej.17.1.200) — Martin (2011), *EMBnet.journal* 17(1):10–12; primer/adapter trimming, used at Stage 4. - Network accessline 495
- [seqkit](https://doi.org/10.1371/journal.pone.0163962) — Shen et al. (2016), *PLoS ONE* 11(10):e0163962; fast FASTQ statistics, used at Stages 1, 3, 5. - Network accessline 495
- [seqkit](https://doi.org/10.1371/journal.pone.0163962) — Shen et al. (2016), *PLoS ONE* 11(10):e0163962; fast FASTQ statistics, used at Stages 1, 3, 5.
skills/claw-amplicon-qc/amplicon_qc.R
skills/claw-amplicon-qc/tests/fixtures/README.md
- Network accessline 7
Derived from a subset of sample B4 from astrobiomike's Deep Sea Rock 16S tutorial dataset (https://astrobiomike.github.io/amplicon/dada2_workflow_ex), - Network accessline 7
Derived from a subset of sample B4 from astrobiomike's Deep Sea Rock 16S tutorial dataset (https://astrobiomike.github.io/amplicon/dada2_workflow_ex), - Network accessline 8
tutorial dataset (https://astrobiomike.github.io/amplicon/dada2_workflow_ex), - Network accessline 8
tutorial dataset (https://astrobiomike.github.io/amplicon/dada2_workflow_ex),
skills/claw-amplicon-qc/tests/preflight_diagnostic.R
skills/claw-amplicon-qc/tests/run_test.sh
skills/claw-ancestry-pca/SKILL.md
- Network accessline 39
category: bioinformatics emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 39
category: bioinformatics emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 40
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 40
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 41
homepage: https://github.com/ClawBio/ClawBio - Network accessline 41
homepage: https://github.com/ClawBio/ClawBio - Network accessline 175
- Mallick, S. et al. (2016). The Simons Genome Diversity Project. Nature, 538, 201-206. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 175
- Mallick, S. et al. (2016). The Simons Genome Diversity Project. Nature, 538, 201-206. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 176
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 176
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/claw-ancestry-pca/ancestry_pca.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 335
- Mallick, S. et al. (2016). The Simons Genome Diversity Project. Nature, 538, 201-206. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 335
- Mallick, S. et al. (2016). The Simons Genome Diversity Project. Nature, 538, 201-206. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 336
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 336
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/claw-ancestry-pca/tests/__init__.py
skills/claw-ancestry-pca/tests/test_ancestry_pca.py
skills/claw-metagenomics/SKILL.md
- Network accessline 63
category: bioinformatics emoji: 🦠 homepage: https://github.com/ClawBio/ClawBio - Network accessline 63
category: bioinformatics emoji: 🦠 homepage: https://github.com/ClawBio/ClawBio - Network accessline 64
emoji: 🦠 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 64
emoji: 🦠 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 65
homepage: https://github.com/ClawBio/ClawBio - Network accessline 65
homepage: https://github.com/ClawBio/ClawBio - Network accessline 271
- Alcock, B.P. et al. (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D419-D430. - Beghini, F. et al. (2021). - Network accessline 271
- Alcock, B.P. et al. (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research, 51(D1), D419-D430. - Beghini, F. et al. (2021). - Network accessline 273
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 273
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/claw-metagenomics/metagenomics_profiler.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 873
- Alcock, B.P. et al. (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. *Nucleic Acids Research*, 51(D1), D419-D430. - Beghini, F. et al. (2021) - Network accessline 873
- Alcock, B.P. et al. (2023). CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database. *Nucleic Acids Research*, 51(D1), D419-D430. - Beghini, F. et al. (2021) - Network accessline 874
- Beghini, F. et al. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. *eLife*, 10, e65088. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio """ - Network accessline 874
- Beghini, F. et al. (2021). Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. *eLife*, 10, e65088. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio """ - Network accessline 875
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 875
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Access to secretsline 1171
[Credential-related source omitted] - Access to secretsline 1171
[Credential-related source omitted] - Access to secretsline 1228
[Credential-related source omitted] - Access to secretsline 1228
[Credential-related source omitted]
skills/claw-methylation-cycle/SKILL.md
- Network accessline 11
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 11
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 12
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
homepage: https://github.com/ClawBio/ClawBio - Network accessline 392
- Spuch C, Agis-Balboa RC. (2014). Epigenetica en neurociencias. *SEBBM*, 179:18-21. - Green RC et al. (2013). ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. *Genet Med*, 15(7):565-74. - C - Network accessline 392
- Spuch C, Agis-Balboa RC. (2014). Epigenetica en neurociencias. *SEBBM*, 179:18-21. - Green RC et al. (2013). ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. *Genet Med*, 15(7):565-74. - C - Network accessline 394
- ClawBio (2026). https://github.com/ClawBio/ClawBio - Network accessline 394
- ClawBio (2026). https://github.com/ClawBio/ClawBio
skills/claw-methylation-cycle/methylation_cycle.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 646
"- Spuch C, Agis-Balboa RC. (2014). Epigenetica en neurociencias. SEBBM 179:18-21.", "- Carmona Aguirre S. (2014/UNESCO 2016). Holomedicina. UNIMED Consulting.", "- ClawBio (2026). https://github.com/ClawBio/ClawBio", - Network accessline 646
"- Spuch C, Agis-Balboa RC. (2014). Epigenetica en neurociencias. SEBBM 179:18-21.", "- Carmona Aguirre S. (2014/UNESCO 2016). Holomedicina. UNIMED Consulting.", "- ClawBio (2026). https://github.com/ClawBio/ClawBio", - Network accessline 647
"- Carmona Aguirre S. (2014/UNESCO 2016). Holomedicina. UNIMED Consulting.", "- ClawBio (2026). https://github.com/ClawBio/ClawBio", ] - Network accessline 647
"- Carmona Aguirre S. (2014/UNESCO 2016). Holomedicina. UNIMED Consulting.", "- ClawBio (2026). https://github.com/ClawBio/ClawBio", ] - Network accessline 648
"- ClawBio (2026). https://github.com/ClawBio/ClawBio", - Network accessline 648
"- ClawBio (2026). https://github.com/ClawBio/ClawBio",
skills/claw-methylation-cycle/tests/test_methylation_cycle.py
skills/claw-methylation-cycle/tests/test_reproducibility_bundle.py
skills/claw-semantic-sim/SKILL.md
- Network accessline 18
always: false emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
always: false emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 20
homepage: https://github.com/ClawBio/ClawBio - Network accessline 20
homepage: https://github.com/ClawBio/ClawBio - Network accessline 146
- Corpas, M. et al. (2026). HEIM: Health Equity Index for Measuring structural bias in biomedical research. Under review. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 146
- Corpas, M. et al. (2026). HEIM: Health Equity Index for Measuring structural bias in biomedical research. Under review. - Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 147
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 147
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio
skills/clawpathy-autoresearch/SKILL.md
- Network accessline 12
always: false emoji: 🔁 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🔁 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🔁 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
emoji: 🔁 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio
skills/clawpathy-autoresearch/__init__.py
skills/clawpathy-autoresearch/__main__.py
skills/clawpathy-autoresearch/dispatcher.py
skills/clawpathy-autoresearch/examples/champions/README.md
- Network accessline 18
ref: str = "main") -> Path: """Download a champion SKILL.md from the ClawBio repo.""" url = (f"https://raw.githubusercontent.com/ClawBio/ClawBio/{ref}" - Network accessline 18
ref: str = "main") -> Path: """Download a champion SKILL.md from the ClawBio repo.""" url = (f"https://raw.githubusercontent.com/ClawBio/ClawBio/{ref}" - Network accessline 19
"""Download a champion SKILL.md from the ClawBio repo.""" url = (f"https://raw.githubusercontent.com/ClawBio/ClawBio/{ref}" f"/skills/clawpathy_autoresearch/examples/champions/{name}.md") - Network accessline 19
"""Download a champion SKILL.md from the ClawBio repo.""" url = (f"https://raw.githubusercontent.com/ClawBio/ClawBio/{ref}" f"/skills/clawpathy_autoresearch/examples/champions/{name}.md") - Network accessline 20
url = (f"https://raw.githubusercontent.com/ClawBio/ClawBio/{ref}" - Network accessline 20
url = (f"https://raw.githubusercontent.com/ClawBio/ClawBio/{ref}" - Network accessline 22
out = Path(dest) / f"{name}.md" out.parent.mkdir(parents=True, exist_ok=True) with urllib.request.urlopen(url) as r: - Network accessline 22
out = Path(dest) / f"{name}.md" out.parent.mkdir(parents=True, exist_ok=True) with urllib.request.urlopen(url) as r: - Network accessline 23
out.parent.mkdir(parents=True, exist_ok=True) with urllib.request.urlopen(url) as r: out.write_bytes(r.read()) - Network accessline 23
out.parent.mkdir(parents=True, exist_ok=True) with urllib.request.urlopen(url) as r: out.write_bytes(r.read()) - Network accessline 24
with urllib.request.urlopen(url) as r: - Network accessline 24
with urllib.request.urlopen(url) as r: - Network accessline 31
curl -sL -o trubetskoy.md \ - Network accessline 31
curl -sL -o trubetskoy.md \ - Network accessline 32
https://raw.githubusercontent.com/ClawBio/ClawBio/main/skills/clawpathy_autoresearch/examples/champions/trubetskoy_scz_finemap_0.235.md - Network accessline 32
https://raw.githubusercontent.com/ClawBio/ClawBio/main/skills/clawpathy_autoresearch/examples/champions/trubetskoy_scz_finemap_0.235.md
skills/clawpathy-autoresearch/examples/champions/trubetskoy_scz_finemap_0.235.md
- Network accessline 109
# FINEMAP v1.4 wget http://www.christianbenner.com/finemap_v1.4_x86_64.tgz -O output/env/finemap_v1.4_x86_64.tgz - Network accessline 109
# FINEMAP v1.4 wget http://www.christianbenner.com/finemap_v1.4_x86_64.tgz -O output/env/finemap_v1.4_x86_64.tgz - Network accessline 110
wget http://www.christianbenner.com/finemap_v1.4_x86_64.tgz -O output/env/finemap_v1.4_x86_64.tgz - Network accessline 110
wget http://www.christianbenner.com/finemap_v1.4_x86_64.tgz -O output/env/finemap_v1.4_x86_64.tgz - Network accessline 171
"pgc3_scz_sumstats": { "path": sys.argv[1], "sha256": sha256(sys.argv[1]), "source_url": "https://pgc.unc.edu/for-researchers/download-results/", - Network accessline 171
"pgc3_scz_sumstats": { "path": sys.argv[1], "sha256": sha256(sys.argv[1]), "source_url": "https://pgc.unc.edu/for-researchers/download-results/", - Network accessline 172
"path": sys.argv[1], "sha256": sha256(sys.argv[1]), "source_url": "https://pgc.unc.edu/for-researchers/download-results/", "retrieval_date": sys.argv[2], "build": "GRCh37", - Network accessline 172
"path": sys.argv[1], "sha256": sha256(sys.argv[1]), "source_url": "https://pgc.unc.edu/for-researchers/download-results/", "retrieval_date": sys.argv[2], "build": "GRCh37", - Network accessline 173
"source_url": "https://pgc.unc.edu/for-researchers/download-results/", - Network accessline 173
"source_url": "https://pgc.unc.edu/for-researchers/download-results/", - Network accessline 182
"path": "output/env/finemap_v1.4_x86_64/finemap_v1.4_x86_64", "sha256": sha256("output/env/finemap_v1.4_x86_64/finemap_v1.4_x86_64"), "source_url": "http://www.christianbenner.com/finemap_v1.4_x86_64.tgz", - Network accessline 182
"path": "output/env/finemap_v1.4_x86_64/finemap_v1.4_x86_64", "sha256": sha256("output/env/finemap_v1.4_x86_64/finemap_v1.4_x86_64"), "source_url": "http://www.christianbenner.com/finemap_v1.4_x86_64.tgz", - Network accessline 183
"sha256": sha256("output/env/finemap_v1.4_x86_64/finemap_v1.4_x86_64"), "source_url": "http://www.christianbenner.com/finemap_v1.4_x86_64.tgz", "version": "1.4", - Network accessline 183
"sha256": sha256("output/env/finemap_v1.4_x86_64/finemap_v1.4_x86_64"), "source_url": "http://www.christianbenner.com/finemap_v1.4_x86_64.tgz", "version": "1.4", - Network accessline 184
"source_url": "http://www.christianbenner.com/finemap_v1.4_x86_64.tgz", - Network accessline 184
"source_url": "http://www.christianbenner.com/finemap_v1.4_x86_64.tgz", - Network accessline 403
for CHR in $(seq 1 22); do F="ALL.chr${CHR}.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz" wget -c "${BASE}/${F}" -O "data/1kg_eur/${F}" - Network accessline 403
for CHR in $(seq 1 22); do F="ALL.chr${CHR}.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz" wget -c "${BASE}/${F}" -O "data/1kg_eur/${F}" - Network accessline 404
F="ALL.chr${CHR}.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz" wget -c "${BASE}/${F}" -O "data/1kg_eur/${F}" wget -c "${BASE}/${F}.tbi" -O "data/1kg_eur/${F}.tbi" - Network accessline 404
F="ALL.chr${CHR}.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz" wget -c "${BASE}/${F}" -O "data/1kg_eur/${F}" wget -c "${BASE}/${F}.tbi" -O "data/1kg_eur/${F}.tbi" - Network accessline 405
wget -c "${BASE}/${F}" -O "data/1kg_eur/${F}" - Network accessline 405
wget -c "${BASE}/${F}" -O "data/1kg_eur/${F}" - Network accessline 406
wget -c "${BASE}/${F}.tbi" -O "data/1kg_eur/${F}.tbi" - Network accessline 406
wget -c "${BASE}/${F}.tbi" -O "data/1kg_eur/${F}.tbi" - Network accessline 408
done PANEL=data/1kg_eur/integrated_call_samples_v3.20130502.ALL.panel wget -c "${BASE}/$(basename $PANEL)" -O $PANEL - Network accessline 408
done PANEL=data/1kg_eur/integrated_call_samples_v3.20130502.ALL.panel wget -c "${BASE}/$(basename $PANEL)" -O $PANEL - Network accessline 409
PANEL=data/1kg_eur/integrated_call_samples_v3.20130502.ALL.panel wget -c "${BASE}/$(basename $PANEL)" -O $PANEL sha256sum $PANEL >> output/provenance/1kg_checksums.txt - Network accessline 409
PANEL=data/1kg_eur/integrated_call_samples_v3.20130502.ALL.panel wget -c "${BASE}/$(basename $PANEL)" -O $PANEL sha256sum $PANEL >> output/provenance/1kg_checksums.txt - Network accessline 410
wget -c "${BASE}/$(basename $PANEL)" -O $PANEL - Network accessline 410
wget -c "${BASE}/$(basename $PANEL)" -O $PANEL
skills/clawpathy-autoresearch/examples/champions/yengo_height_ldsc_h2.md
- Network accessline 127
done echo "BaselineLD missing: $BASELINE_MISSING" | tee -a $OUT/env/ld_preflight.txt [ $BASELINE_MISSING -gt 0 ] && { echo "GATE HARD FAIL: no usable LD reference — re-stage from https://data.broadinstitute.org/alkesgroup/LDSCORE/"; exit 1; - Network accessline 127
done echo "BaselineLD missing: $BASELINE_MISSING" | tee -a $OUT/env/ld_preflight.txt [ $BASELINE_MISSING -gt 0 ] && { echo "GATE HARD FAIL: no usable LD reference — re-stage from https://data.broadinstitute.org/alkesgroup/LDSCORE/"; exit 1; - Network accessline 129
[ $BASELINE_MISSING -gt 0 ] && { echo "GATE HARD FAIL: no usable LD reference — re-stage from https://data.broadinstitute.org/alkesgroup/LDSCORE/"; exit 1; } - Network accessline 129
[ $BASELINE_MISSING -gt 0 ] && { echo "GATE HARD FAIL: no usable LD reference — re-stage from https://data.broadinstitute.org/alkesgroup/LDSCORE/"; exit 1; }
skills/clawpathy-autoresearch/executor.py
skills/clawpathy-autoresearch/judge.py
skills/clawpathy-autoresearch/loop.py
skills/clawpathy-autoresearch/loop_parallel.py
skills/clawpathy-autoresearch/multitask_loop.py
skills/clawpathy-autoresearch/proposer.py
skills/clawpathy-autoresearch/workspace.py
skills/clinical-trial-finder/SKILL.md
- Network accessline 86
always: false emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio - Network accessline 86
always: false emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio - Network accessline 87
emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 87
emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 88
homepage: https://github.com/ClawBio/ClawBio - Network accessline 88
homepage: https://github.com/ClawBio/ClawBio - Network accessline 107
- **Source database**: ClinicalTrials.gov API v2 (`https://clinicaltrials.gov/api/v2`) — the authoritative US registry mandated by FDAAA 801 (2007) and mirrored by WHO ICTRP. Chosen over EudraCT/EUCTR because it covers the largest global tr - Network accessline 107
- **Source database**: ClinicalTrials.gov API v2 (`https://clinicaltrials.gov/api/v2`) — the authoritative US registry mandated by FDAAA 801 (2007) and mirrored by WHO ICTRP. Chosen over EudraCT/EUCTR because it covers the largest global tr - Network accessline 109
- **Query field**: `query.cond` (condition/disease field), not `query.term` (free-text across all fields). `query.cond` is indexed against MeSH descriptors by the NLM indexing pipeline, giving substantially better recall for condition queri - Network accessline 109
- **Query field**: `query.cond` (condition/disease field), not `query.term` (free-text across all fields). `query.cond` is indexed against MeSH descriptors by the NLM indexing pipeline, giving substantially better recall for condition queri - Network accessline 111
- **MeSH condition coding**: MeSH IDs are read from `derivedSection.conditionBrowseModule.meshes` — the NLM-curated MeSH mapping that ClinicalTrials.gov computes internally during study indexing. This avoids a separate NLM API call and uses - Network accessline 111
- **MeSH condition coding**: MeSH IDs are read from `derivedSection.conditionBrowseModule.meshes` — the NLM-curated MeSH mapping that ClinicalTrials.gov computes internally during study indexing. This avoids a separate NLM API call and uses - Network accessline 119
- **FHIR version**: FHIR R4, not R5. The ONC 21st Century Cures Act Final Rule (2020) mandates FHIR R4 for certified EHR systems in the US, making R4 the de facto standard for EHR interoperability with Epic, Cerner, and Oracle Health. R5 is - Network accessline 119
- **FHIR version**: FHIR R4, not R5. The ONC 21st Century Cures Act Final Rule (2020) mandates FHIR R4 for certified EHR systems in the US, making R4 the de facto standard for EHR interoperability with Epic, Cerner, and Oracle Health. R5 is - Network accessline 121
- **FHIR resource type**: `ResearchStudy` — the canonical HL7 FHIR R4 resource for clinical trials. Status and phase codes map verbatim from the published R4 value sets: `research-study-status` (`http://hl7.org/fhir/research-study-status`) - Network accessline 121
- **FHIR resource type**: `ResearchStudy` — the canonical HL7 FHIR R4 resource for clinical trials. Status and phase codes map verbatim from the published R4 value sets: `research-study-status` (`http://hl7.org/fhir/research-study-status`) - Network accessline 125
- **Association score threshold**: ≥ 0.6 (`--ot-min-score`). The OpenTargets overall association score is a harmonic sum across evidence types, normalised to [0, 1]. Scores < 0.5 typically reflect single-source, indirect, or low-confidence - Network accessline 125
- **Association score threshold**: ≥ 0.6 (`--ot-min-score`). The OpenTargets overall association score is a harmonic sum across evidence types, normalised to [0, 1]. Scores < 0.5 typically reflect single-source, indirect, or low-confidence
skills/clinical-trial-finder/api.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 34
for attempt in range(_MAX_RETRIES): try: with urllib.request.urlopen(url, timeout=timeout) as resp: - Network accessline 34
for attempt in range(_MAX_RETRIES): try: with urllib.request.urlopen(url, timeout=timeout) as resp: - Network accessline 35
try: with urllib.request.urlopen(url, timeout=timeout) as resp: return resp.read() - Network accessline 35
try: with urllib.request.urlopen(url, timeout=timeout) as resp: return resp.read() - Network accessline 36
with urllib.request.urlopen(url, timeout=timeout) as resp: - Network accessline 36
with urllib.request.urlopen(url, timeout=timeout) as resp:
skills/clinical-trial-finder/clinical_trial_finder.py
skills/clinical-trial-finder/constants.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 23
CT_API = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 23
CT_API = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 252
EUCTR_API = "https://www.clinicaltrialsregister.eu/ctr-search/rest/search?query=" - Network accessline 252
EUCTR_API = "https://www.clinicaltrialsregister.eu/ctr-search/rest/search?query="
skills/clinical-trial-finder/demo.sh
skills/clinical-trial-finder/euctr.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 40
try: req = urllib.request.Request(url, headers={"Accept": "application/xml"}) - Network accessline 40
try: req = urllib.request.Request(url, headers={"Accept": "application/xml"}) - Network accessline 41
req = urllib.request.Request(url, headers={"Accept": "application/xml"}) - Network accessline 41
req = urllib.request.Request(url, headers={"Accept": "application/xml"}) - Network accessline 42
with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 42
with urllib.request.urlopen(req, timeout=10) as resp:
skills/clinical-trial-finder/examples/demo_output/commands.sh
skills/clinical-trial-finder/examples/demo_output/fhir_bundle.json
- Network accessline 6
"entry": [ { "fullUrl": "https://clinicaltrials.gov/study/NCT00555503", - Network accessline 6
"entry": [ { "fullUrl": "https://clinicaltrials.gov/study/NCT00555503", - Network accessline 7
{ "fullUrl": "https://clinicaltrials.gov/study/NCT00555503", "resource": { - Network accessline 7
{ "fullUrl": "https://clinicaltrials.gov/study/NCT00555503", "resource": { - Network accessline 8
"fullUrl": "https://clinicaltrials.gov/study/NCT00555503", - Network accessline 8
"fullUrl": "https://clinicaltrials.gov/study/NCT00555503", - Network accessline 12
"meta": { "profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 12
"meta": { "profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 13
"profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" ] - Network accessline 13
"profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" ] - Network accessline 14
"http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 14
"http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 18
{ "use": "official", "system": "https://clinicaltrials.gov", - Network accessline 18
{ "use": "official", "system": "https://clinicaltrials.gov", - Network accessline 19
"use": "official", "system": "https://clinicaltrials.gov", "value": "NCT00555503" - Network accessline 19
"use": "official", "system": "https://clinicaltrials.gov", "value": "NCT00555503" - Network accessline 20
"system": "https://clinicaltrials.gov", - Network accessline 20
"system": "https://clinicaltrials.gov", - Network accessline 27
"coding": [ { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 27
"coding": [ { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 28
{ "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", "code": "n-a", - Network accessline 28
{ "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", "code": "n-a", - Network accessline 29
"system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 29
"system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 37
"coding": [ { "system": "http://clinicaltrials.gov/study-type", - Network accessline 37
"coding": [ { "system": "http://clinicaltrials.gov/study-type", - Network accessline 38
{ "system": "http://clinicaltrials.gov/study-type", "code": "OBSERVATIONAL", - Network accessline 38
{ "system": "http://clinicaltrials.gov/study-type", "code": "OBSERVATIONAL", - Network accessline 39
"system": "http://clinicaltrials.gov/study-type", - Network accessline 39
"system": "http://clinicaltrials.gov/study-type", - Network accessline 48
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 48
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 49
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D001943", - Network accessline 49
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D001943", - Network accessline 50
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 50
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 58
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 58
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 59
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D020022", - Network accessline 59
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D020022", - Network accessline 60
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 60
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 68
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 68
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 69
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D000275", - Network accessline 69
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D000275", - Network accessline 70
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 70
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 84
}, { "fullUrl": "https://clinicaltrials.gov/study/NCT01102569", - Network accessline 84
}, { "fullUrl": "https://clinicaltrials.gov/study/NCT01102569", - Network accessline 85
{ "fullUrl": "https://clinicaltrials.gov/study/NCT01102569", "resource": { - Network accessline 85
{ "fullUrl": "https://clinicaltrials.gov/study/NCT01102569", "resource": { - Network accessline 86
"fullUrl": "https://clinicaltrials.gov/study/NCT01102569", - Network accessline 86
"fullUrl": "https://clinicaltrials.gov/study/NCT01102569", - Network accessline 90
"meta": { "profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 90
"meta": { "profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 91
"profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" ] - Network accessline 91
"profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" ] - Network accessline 92
"http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 92
"http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 96
{ "use": "official", "system": "https://clinicaltrials.gov", - Network accessline 96
{ "use": "official", "system": "https://clinicaltrials.gov", - Network accessline 97
"use": "official", "system": "https://clinicaltrials.gov", "value": "NCT01102569" - Network accessline 97
"use": "official", "system": "https://clinicaltrials.gov", "value": "NCT01102569" - Network accessline 98
"system": "https://clinicaltrials.gov", - Network accessline 98
"system": "https://clinicaltrials.gov", - Network accessline 105
"coding": [ { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 105
"coding": [ { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 106
{ "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", "code": "n-a", - Network accessline 106
{ "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", "code": "n-a", - Network accessline 107
"system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 107
"system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 115
"coding": [ { "system": "http://clinicaltrials.gov/study-type", - Network accessline 115
"coding": [ { "system": "http://clinicaltrials.gov/study-type", - Network accessline 116
{ "system": "http://clinicaltrials.gov/study-type", "code": "OBSERVATIONAL", - Network accessline 116
{ "system": "http://clinicaltrials.gov/study-type", "code": "OBSERVATIONAL", - Network accessline 117
"system": "http://clinicaltrials.gov/study-type", - Network accessline 117
"system": "http://clinicaltrials.gov/study-type", - Network accessline 126
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 126
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 127
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D010190", - Network accessline 127
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "D010190", - Network accessline 128
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 128
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 136
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 136
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 137
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "C535837", - Network accessline 137
{ "system": "http://id.nlm.nih.gov/mesh/", "code": "C535837", - Network accessline 138
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 138
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 152
}, { "fullUrl": "https://clinicaltrials.gov/study/NCT04584255", - Network accessline 152
}, { "fullUrl": "https://clinicaltrials.gov/study/NCT04584255", - Network accessline 153
{ "fullUrl": "https://clinicaltrials.gov/study/NCT04584255", "resource": { - Network accessline 153
{ "fullUrl": "https://clinicaltrials.gov/study/NCT04584255", "resource": { - Network accessline 154
"fullUrl": "https://clinicaltrials.gov/study/NCT04584255", - Network accessline 154
"fullUrl": "https://clinicaltrials.gov/study/NCT04584255", - Network accessline 158
"meta": { "profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 158
"meta": { "profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 159
"profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" ] - Network accessline 159
"profile": [ "http://hl7.org/fhir/StructureDefinition/ResearchStudy" ] - Network accessline 160
"http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 160
"http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 164
{ "use": "official", "system": "https://clinicaltrials.gov", - Network accessline 164
{ "use": "official", "system": "https://clinicaltrials.gov", - Network accessline 165
"use": "official", "system": "https://clinicaltrials.gov", "value": "NCT04584255" - Network accessline 165
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- Network accessline 57
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT00555503" target="_blank">Re - Network accessline 57
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT00555503" target="_blank">Re - Network accessline 58
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT00555503" target="_blank">Registry of Mastectomy for Breast Cancer Risk Reduction</a> </div> - Network accessline 58
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT00555503" target="_blank">Registry of Mastectomy for Breast Cancer Risk Reduction</a> </div> - Network accessline 59
<a href="https://clinicaltrials.gov/study/NCT00555503" target="_blank">Registry of Mastectomy for Breast Cancer Risk Reduction</a> - Network accessline 59
<a href="https://clinicaltrials.gov/study/NCT00555503" target="_blank">Registry of Mastectomy for Breast Cancer Risk Reduction</a> - Network accessline 71
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT01102569" target="_blank">P - Network accessline 71
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT01102569" target="_blank">P - Network accessline 72
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT01102569" target="_blank">Pancreatic Cancer Genetics</a> </div> - Network accessline 72
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT01102569" target="_blank">Pancreatic Cancer Genetics</a> </div> - Network accessline 73
<a href="https://clinicaltrials.gov/study/NCT01102569" target="_blank">Pancreatic Cancer Genetics</a> - Network accessline 73
<a href="https://clinicaltrials.gov/study/NCT01102569" target="_blank">Pancreatic Cancer Genetics</a> - Network accessline 85
<span style="background:#f1c40f;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04584255" target - Network accessline 85
<span style="background:#f1c40f;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04584255" target - Network accessline 86
font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04584255" target="_blank">Niraparib + Dostarlimab In BRCA Mutated Breast Cancer</a> </div> - Network accessline 86
font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04584255" target="_blank">Niraparib + Dostarlimab In BRCA Mutated Breast Cancer</a> </div> - Network accessline 87
<a href="https://clinicaltrials.gov/study/NCT04584255" target="_blank">Niraparib + Dostarlimab In BRCA Mutated Breast Cancer</a> - Network accessline 87
<a href="https://clinicaltrials.gov/study/NCT04584255" target="_blank">Niraparib + Dostarlimab In BRCA Mutated Breast Cancer</a> - Network accessline 99
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT03475979" target="_blank">Abbr - Network accessline 99
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT03475979" target="_blank">Abbr - Network accessline 100
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT03475979" target="_blank">Abbreviated Breast MRI for Second Breast Cancer Detection in Women With BRCA Mutation Testing</a> - Network accessline 100
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT03475979" target="_blank">Abbreviated Breast MRI for Second Breast Cancer Detection in Women With BRCA Mutation Testing</a> - Network accessline 101
<a href="https://clinicaltrials.gov/study/NCT03475979" target="_blank">Abbreviated Breast MRI for Second Breast Cancer Detection in Women With BRCA Mutation Testing</a> - Network accessline 101
<a href="https://clinicaltrials.gov/study/NCT03475979" target="_blank">Abbreviated Breast MRI for Second Breast Cancer Detection in Women With BRCA Mutation Testing</a> - Network accessline 113
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02365805" target="_blank">Ra - Network accessline 113
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02365805" target="_blank">Ra - Network accessline 114
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02365805" target="_blank">Randomized CT to Evaluate Efficacy of Neoadjuvant Chemotherapy Customized by Levels of BRCA1-HER2 Negative - Network accessline 114
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02365805" target="_blank">Randomized CT to Evaluate Efficacy of Neoadjuvant Chemotherapy Customized by Levels of BRCA1-HER2 Negative - Network accessline 115
<a href="https://clinicaltrials.gov/study/NCT02365805" target="_blank">Randomized CT to Evaluate Efficacy of Neoadjuvant Chemotherapy Customized by Levels of BRCA1-HER2 Negative Breast Cancer</a> - Network accessline 115
<a href="https://clinicaltrials.gov/study/NCT02365805" target="_blank">Randomized CT to Evaluate Efficacy of Neoadjuvant Chemotherapy Customized by Levels of BRCA1-HER2 Negative Breast Cancer</a> - Network accessline 127
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT04296370" target="_blank">A St - Network accessline 127
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT04296370" target="_blank">A St - Network accessline 128
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT04296370" target="_blank">A Study of Fluzoparib±Apatinib Versus Chemotherapy Treatment of Physician's Choice in HER2-negative Met - Network accessline 128
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT04296370" target="_blank">A Study of Fluzoparib±Apatinib Versus Chemotherapy Treatment of Physician's Choice in HER2-negative Met - Network accessline 129
<a href="https://clinicaltrials.gov/study/NCT04296370" target="_blank">A Study of Fluzoparib±Apatinib Versus Chemotherapy Treatment of Physician's Choice in HER2-negative Metastatic Breast Cancer Patients With Germline BRCA Mutation</a - Network accessline 129
<a href="https://clinicaltrials.gov/study/NCT04296370" target="_blank">A Study of Fluzoparib±Apatinib Versus Chemotherapy Treatment of Physician's Choice in HER2-negative Metastatic Breast Cancer Patients With Germline BRCA Mutation</a - Network accessline 141
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT03495609" target="_blank">Us - Network accessline 141
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT03495609" target="_blank">Us - Network accessline 142
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT03495609" target="_blank">Use of Recombinant hCG to Prevent Breast Cancer in BRCA1 and BRCA2 Carriers</a> </div> - Network accessline 142
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT03495609" target="_blank">Use of Recombinant hCG to Prevent Breast Cancer in BRCA1 and BRCA2 Carriers</a> </div> - Network accessline 143
<a href="https://clinicaltrials.gov/study/NCT03495609" target="_blank">Use of Recombinant hCG to Prevent Breast Cancer in BRCA1 and BRCA2 Carriers</a> - Network accessline 143
<a href="https://clinicaltrials.gov/study/NCT03495609" target="_blank">Use of Recombinant hCG to Prevent Breast Cancer in BRCA1 and BRCA2 Carriers</a> - Network accessline 155
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04150042" target="_blank">S - Network accessline 155
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04150042" target="_blank">S - Network accessline 156
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04150042" target="_blank">SHARON: A Clinical Trial for Metastatic Cancer Using Chemotherapy and Patients' Own Stem Cells</a> - Network accessline 156
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04150042" target="_blank">SHARON: A Clinical Trial for Metastatic Cancer Using Chemotherapy and Patients' Own Stem Cells</a> - Network accessline 157
<a href="https://clinicaltrials.gov/study/NCT04150042" target="_blank">SHARON: A Clinical Trial for Metastatic Cancer Using Chemotherapy and Patients' Own Stem Cells</a> - Network accessline 157
<a href="https://clinicaltrials.gov/study/NCT04150042" target="_blank">SHARON: A Clinical Trial for Metastatic Cancer Using Chemotherapy and Patients' Own Stem Cells</a> - Network accessline 169
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT00823654" target="_blank">S - Network accessline 169
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT00823654" target="_blank">S - Network accessline 170
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT00823654" target="_blank">Serum Biomarkers to Characterize the Effects of Therapy on Ovarian Reserve in Premenopausal Women With Ea - Network accessline 170
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT00823654" target="_blank">Serum Biomarkers to Characterize the Effects of Therapy on Ovarian Reserve in Premenopausal Women With Ea - Network accessline 171
<a href="https://clinicaltrials.gov/study/NCT00823654" target="_blank">Serum Biomarkers to Characterize the Effects of Therapy on Ovarian Reserve in Premenopausal Women With Early-stage Breast Cancer or BRCA Mutations</a> - Network accessline 171
<a href="https://clinicaltrials.gov/study/NCT00823654" target="_blank">Serum Biomarkers to Characterize the Effects of Therapy on Ovarian Reserve in Premenopausal Women With Early-stage Breast Cancer or BRCA Mutations</a> - Network accessline 183
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05763472" target="_blank">Brea - Network accessline 183
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05763472" target="_blank">Brea - Network accessline 184
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05763472" target="_blank">Breast Cancer After Ovarian Cancer During and/or After Therapy: Genomic Evaluation</a> </div> - Network accessline 184
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05763472" target="_blank">Breast Cancer After Ovarian Cancer During and/or After Therapy: Genomic Evaluation</a> </div> - Network accessline 185
<a href="https://clinicaltrials.gov/study/NCT05763472" target="_blank">Breast Cancer After Ovarian Cancer During and/or After Therapy: Genomic Evaluation</a> - Network accessline 185
<a href="https://clinicaltrials.gov/study/NCT05763472" target="_blank">Breast Cancer After Ovarian Cancer During and/or After Therapy: Genomic Evaluation</a> - Network accessline 197
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02418624" target="_blank">Ph - Network accessline 197
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02418624" target="_blank">Ph - Network accessline 198
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02418624" target="_blank">Phase I of Carboplatin-Olaparib Followed by Olaparib Monotherapy in Advanced Cancer</a> </div> - Network accessline 198
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT02418624" target="_blank">Phase I of Carboplatin-Olaparib Followed by Olaparib Monotherapy in Advanced Cancer</a> </div> - Network accessline 199
<a href="https://clinicaltrials.gov/study/NCT02418624" target="_blank">Phase I of Carboplatin-Olaparib Followed by Olaparib Monotherapy in Advanced Cancer</a> - Network accessline 199
<a href="https://clinicaltrials.gov/study/NCT02418624" target="_blank">Phase I of Carboplatin-Olaparib Followed by Olaparib Monotherapy in Advanced Cancer</a> - Network accessline 211
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05409222" target="_blank">Stud - Network accessline 211
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05409222" target="_blank">Stud - Network accessline 212
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05409222" target="_blank">Study of Quality of Life Post Salpingo-oophorectomy in BRCA1/2 & PALB2 Mutation Carriers (BRCA-HRT)</a> - Network accessline 212
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT05409222" target="_blank">Study of Quality of Life Post Salpingo-oophorectomy in BRCA1/2 & PALB2 Mutation Carriers (BRCA-HRT)</a> - Network accessline 213
<a href="https://clinicaltrials.gov/study/NCT05409222" target="_blank">Study of Quality of Life Post Salpingo-oophorectomy in BRCA1/2 & PALB2 Mutation Carriers (BRCA-HRT)</a> - Network accessline 213
<a href="https://clinicaltrials.gov/study/NCT05409222" target="_blank">Study of Quality of Life Post Salpingo-oophorectomy in BRCA1/2 & PALB2 Mutation Carriers (BRCA-HRT)</a> - Network accessline 225
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT01506609" target="_blank">St - Network accessline 225
<span style="background:#95a5a6;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT01506609" target="_blank">St - Network accessline 226
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT01506609" target="_blank">Study Evaluating Efficacy And Tolerability Of Veliparib in Combination With Temozolomide (TMZ) or In Combi - Network accessline 226
font-size:0.8em;margin-right:8px">COMPLETED</span> <a href="https://clinicaltrials.gov/study/NCT01506609" target="_blank">Study Evaluating Efficacy And Tolerability Of Veliparib in Combination With Temozolomide (TMZ) or In Combi - Network accessline 227
<a href="https://clinicaltrials.gov/study/NCT01506609" target="_blank">Study Evaluating Efficacy And Tolerability Of Veliparib in Combination With Temozolomide (TMZ) or In Combination With Carboplatin and Paclitaxel Versus Placebo in Partic - Network accessline 227
<a href="https://clinicaltrials.gov/study/NCT01506609" target="_blank">Study Evaluating Efficacy And Tolerability Of Veliparib in Combination With Temozolomide (TMZ) or In Combination With Carboplatin and Paclitaxel Versus Placebo in Partic - Network accessline 239
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT00897455" target="_blank">Stud - Network accessline 239
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT00897455" target="_blank">Stud - Network accessline 240
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT00897455" target="_blank">Studying Breast Cancer Risk in Women Who Are BRCA1/BRCA2 Mutation Carriers</a> </div> - Network accessline 240
font-size:0.8em;margin-right:8px">UNKNOWN</span> <a href="https://clinicaltrials.gov/study/NCT00897455" target="_blank">Studying Breast Cancer Risk in Women Who Are BRCA1/BRCA2 Mutation Carriers</a> </div> - Network accessline 241
<a href="https://clinicaltrials.gov/study/NCT00897455" target="_blank">Studying Breast Cancer Risk in Women Who Are BRCA1/BRCA2 Mutation Carriers</a> - Network accessline 241
<a href="https://clinicaltrials.gov/study/NCT00897455" target="_blank">Studying Breast Cancer Risk in Women Who Are BRCA1/BRCA2 Mutation Carriers</a> - Network accessline 253
<span style="background:#f1c40f;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04474834" target - Network accessline 253
<span style="background:#f1c40f;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04474834" target - Network accessline 254
font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04474834" target="_blank">Genetic Risk Estimations for Influencing Decision Making in Women at High Risk of Breast Cance - Network accessline 254
font-size:0.8em;margin-right:8px">ACTIVE_NOT_RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT04474834" target="_blank">Genetic Risk Estimations for Influencing Decision Making in Women at High Risk of Breast Cance - Network accessline 255
<a href="https://clinicaltrials.gov/study/NCT04474834" target="_blank">Genetic Risk Estimations for Influencing Decision Making in Women at High Risk of Breast Cancer, GENRE 2 Study</a> - Network accessline 255
<a href="https://clinicaltrials.gov/study/NCT04474834" target="_blank">Genetic Risk Estimations for Influencing Decision Making in Women at High Risk of Breast Cancer, GENRE 2 Study</a> - Network accessline 267
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT06792721" target="_blank">M - Network accessline 267
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT06792721" target="_blank">M - Network accessline 268
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT06792721" target="_blank">MEASUREMENT OF CIRCULATING MUTATION BURDEN</a> </div> - Network accessline 268
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT06792721" target="_blank">MEASUREMENT OF CIRCULATING MUTATION BURDEN</a> </div> - Network accessline 269
<a href="https://clinicaltrials.gov/study/NCT06792721" target="_blank">MEASUREMENT OF CIRCULATING MUTATION BURDEN</a> - Network accessline 269
<a href="https://clinicaltrials.gov/study/NCT06792721" target="_blank">MEASUREMENT OF CIRCULATING MUTATION BURDEN</a> - Network accessline 281
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT05485766" target="_blank">N - Network accessline 281
<span style="background:#2ecc71;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT05485766" target="_blank">N - Network accessline 282
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT05485766" target="_blank">Novel Neoadjuvant and Adjuvant Strategy for Germline BRCA 1/2 Mutated Triple Negative Breast Cancer</a> - Network accessline 282
font-size:0.8em;margin-right:8px">RECRUITING</span> <a href="https://clinicaltrials.gov/study/NCT05485766" target="_blank">Novel Neoadjuvant and Adjuvant Strategy for Germline BRCA 1/2 Mutated Triple Negative Breast Cancer</a> - Network accessline 283
<a href="https://clinicaltrials.gov/study/NCT05485766" target="_blank">Novel Neoadjuvant and Adjuvant Strategy for Germline BRCA 1/2 Mutated Triple Negative Breast Cancer</a> - Network accessline 283
<a href="https://clinicaltrials.gov/study/NCT05485766" target="_blank">Novel Neoadjuvant and Adjuvant Strategy for Germline BRCA 1/2 Mutated Triple Negative Breast Cancer</a> - Network accessline 295
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">NO_LONGER_AVAILABLE</span> <a href="https://clinicaltrials.gov/study/NCT02985658" target=" - Network accessline 295
<span style="background:#bdc3c7;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">NO_LONGER_AVAILABLE</span> <a href="https://clinicaltrials.gov/study/NCT02985658" target=" - Network accessline 296
font-size:0.8em;margin-right:8px">NO_LONGER_AVAILABLE</span> <a href="https://clinicaltrials.gov/study/NCT02985658" target="_blank">Expanded Access With ABT-888 (Veliparib) to Treat Metastatic Breast Cancer</a> </div> - Network accessline 296
font-size:0.8em;margin-right:8px">NO_LONGER_AVAILABLE</span> <a href="https://clinicaltrials.gov/study/NCT02985658" target="_blank">Expanded Access With ABT-888 (Veliparib) to Treat Metastatic Breast Cancer</a> </div> - Network accessline 297
<a href="https://clinicaltrials.gov/study/NCT02985658" target="_blank">Expanded Access With ABT-888 (Veliparib) to Treat Metastatic Breast Cancer</a> - Network accessline 297
<a href="https://clinicaltrials.gov/study/NCT02985658" target="_blank">Expanded Access With ABT-888 (Veliparib) to Treat Metastatic Breast Cancer</a> - Network accessline 309
<span style="background:#27ae60;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">ENROLLING_BY_INVITATION</span> <a href="https://clinicaltrials.gov/study/NCT07381985" targ - Network accessline 309
<span style="background:#27ae60;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">ENROLLING_BY_INVITATION</span> <a href="https://clinicaltrials.gov/study/NCT07381985" targ - Network accessline 310
font-size:0.8em;margin-right:8px">ENROLLING_BY_INVITATION</span> <a href="https://clinicaltrials.gov/study/NCT07381985" target="_blank">Strategy for Management of Patients With Hereditary Cancer Syndromes (HCS) in a Rural Enviro - Network accessline 310
font-size:0.8em;margin-right:8px">ENROLLING_BY_INVITATION</span> <a href="https://clinicaltrials.gov/study/NCT07381985" target="_blank">Strategy for Management of Patients With Hereditary Cancer Syndromes (HCS) in a Rural Enviro - Network accessline 311
<a href="https://clinicaltrials.gov/study/NCT07381985" target="_blank">Strategy for Management of Patients With Hereditary Cancer Syndromes (HCS) in a Rural Environment</a> - Network accessline 311
<a href="https://clinicaltrials.gov/study/NCT07381985" target="_blank">Strategy for Management of Patients With Hereditary Cancer Syndromes (HCS) in a Rural Environment</a> - Network accessline 323
<span style="background:#e74c3c;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">TERMINATED</span> <a href="https://clinicaltrials.gov/study/NCT01905592" target="_blank">A - Network accessline 323
<span style="background:#e74c3c;color:white;padding:2px 8px;border-radius:3px; font-size:0.8em;margin-right:8px">TERMINATED</span> <a href="https://clinicaltrials.gov/study/NCT01905592" target="_blank">A - Network accessline 324
font-size:0.8em;margin-right:8px">TERMINATED</span> <a href="https://clinicaltrials.gov/study/NCT01905592" target="_blank">A Phase III Trial of Niraparib Versus Physician's Choice in HER2 Negative, Germline BRCA Mutation-po - Network accessline 324
font-size:0.8em;margin-right:8px">TERMINATED</span> <a href="https://clinicaltrials.gov/study/NCT01905592" target="_blank">A Phase III Trial of Niraparib Versus Physician's Choice in HER2 Negative, Germline BRCA Mutation-po - Network accessline 325
<a href="https://clinicaltrials.gov/study/NCT01905592" target="_blank">A Phase III Trial of Niraparib Versus Physician's Choice in HER2 Negative, Germline BRCA Mutation-positive Breast Cancer Patients</a> - Network accessline 325
<a href="https://clinicaltrials.gov/study/NCT01905592" target="_blank">A Phase III Trial of Niraparib Versus Physician's Choice in HER2 Negative, Germline BRCA Mutation-positive Breast Cancer Patients</a>
skills/clinical-trial-finder/examples/demo_output/report.md
- Network accessline 23
- **NCT ID**: [NCT00555503](https://clinicaltrials.gov/study/NCT00555503) - Network accessline 23
- **NCT ID**: [NCT00555503](https://clinicaltrials.gov/study/NCT00555503) - Network accessline 34
- **NCT ID**: [NCT01102569](https://clinicaltrials.gov/study/NCT01102569) - Network accessline 34
- **NCT ID**: [NCT01102569](https://clinicaltrials.gov/study/NCT01102569) - Network accessline 45
- **NCT ID**: [NCT04584255](https://clinicaltrials.gov/study/NCT04584255) - Network accessline 45
- **NCT ID**: [NCT04584255](https://clinicaltrials.gov/study/NCT04584255) - Network accessline 62
- **NCT ID**: [NCT03475979](https://clinicaltrials.gov/study/NCT03475979) - Network accessline 62
- **NCT ID**: [NCT03475979](https://clinicaltrials.gov/study/NCT03475979) - Network accessline 79
- **NCT ID**: [NCT02365805](https://clinicaltrials.gov/study/NCT02365805) - Network accessline 79
- **NCT ID**: [NCT02365805](https://clinicaltrials.gov/study/NCT02365805) - Network accessline 91
- **NCT ID**: [NCT04296370](https://clinicaltrials.gov/study/NCT04296370) - Network accessline 91
- **NCT ID**: [NCT04296370](https://clinicaltrials.gov/study/NCT04296370) - Network accessline 103
- **NCT ID**: [NCT03495609](https://clinicaltrials.gov/study/NCT03495609) - Network accessline 103
- **NCT ID**: [NCT03495609](https://clinicaltrials.gov/study/NCT03495609) - Network accessline 115
- **NCT ID**: [NCT04150042](https://clinicaltrials.gov/study/NCT04150042) - Network accessline 115
- **NCT ID**: [NCT04150042](https://clinicaltrials.gov/study/NCT04150042) - Network accessline 127
- **NCT ID**: [NCT00823654](https://clinicaltrials.gov/study/NCT00823654) - Network accessline 127
- **NCT ID**: [NCT00823654](https://clinicaltrials.gov/study/NCT00823654) - Network accessline 139
- **NCT ID**: [NCT05763472](https://clinicaltrials.gov/study/NCT05763472) - Network accessline 139
- **NCT ID**: [NCT05763472](https://clinicaltrials.gov/study/NCT05763472) - Network accessline 151
- **NCT ID**: [NCT02418624](https://clinicaltrials.gov/study/NCT02418624) - Network accessline 151
- **NCT ID**: [NCT02418624](https://clinicaltrials.gov/study/NCT02418624) - Network accessline 163
- **NCT ID**: [NCT05409222](https://clinicaltrials.gov/study/NCT05409222) - Network accessline 163
- **NCT ID**: [NCT05409222](https://clinicaltrials.gov/study/NCT05409222) - Network accessline 175
- **NCT ID**: [NCT01506609](https://clinicaltrials.gov/study/NCT01506609) - Network accessline 175
- **NCT ID**: [NCT01506609](https://clinicaltrials.gov/study/NCT01506609) - Network accessline 187
- **NCT ID**: [NCT00897455](https://clinicaltrials.gov/study/NCT00897455) - Network accessline 187
- **NCT ID**: [NCT00897455](https://clinicaltrials.gov/study/NCT00897455) - Network accessline 201
- **NCT ID**: [NCT04474834](https://clinicaltrials.gov/study/NCT04474834) - Network accessline 201
- **NCT ID**: [NCT04474834](https://clinicaltrials.gov/study/NCT04474834) - Network accessline 213
- **NCT ID**: [NCT06792721](https://clinicaltrials.gov/study/NCT06792721) - Network accessline 213
- **NCT ID**: [NCT06792721](https://clinicaltrials.gov/study/NCT06792721) - Network accessline 225
- **NCT ID**: [NCT05485766](https://clinicaltrials.gov/study/NCT05485766) - Network accessline 225
- **NCT ID**: [NCT05485766](https://clinicaltrials.gov/study/NCT05485766) - Network accessline 239
- **NCT ID**: [NCT02985658](https://clinicaltrials.gov/study/NCT02985658) - Network accessline 239
- **NCT ID**: [NCT02985658](https://clinicaltrials.gov/study/NCT02985658) - Network accessline 251
- **NCT ID**: [NCT07381985](https://clinicaltrials.gov/study/NCT07381985) - Network accessline 251
- **NCT ID**: [NCT07381985](https://clinicaltrials.gov/study/NCT07381985) - Network accessline 263
- **NCT ID**: [NCT01905592](https://clinicaltrials.gov/study/NCT01905592) - Network accessline 263
- **NCT ID**: [NCT01905592](https://clinicaltrials.gov/study/NCT01905592)
skills/clinical-trial-finder/gwas_bridge.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 19
_GWAS_API = "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 19
_GWAS_API = "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 63
"sort": "p_value", "direction": "asc", }) req = urllib.request.Request( - Network accessline 63
"sort": "p_value", "direction": "asc", }) req = urllib.request.Request( - Network accessline 64
}) req = urllib.request.Request( f"{_GWAS_API}/associations?{query}", headers={"Accept": "application/json"} - Network accessline 64
}) req = urllib.request.Request( f"{_GWAS_API}/associations?{query}", headers={"Accept": "application/json"} - Network accessline 65
req = urllib.request.Request( - Network accessline 65
req = urllib.request.Request( - Network accessline 67
) try: with urllib.request.urlopen(req, timeout=30) as resp: - Network accessline 67
) try: with urllib.request.urlopen(req, timeout=30) as resp: - Network accessline 68
try: with urllib.request.urlopen(req, timeout=30) as resp: data = json.loads(resp.read().decode()) - Network accessline 68
try: with urllib.request.urlopen(req, timeout=30) as resp: data = json.loads(resp.read().decode()) - Network accessline 69
with urllib.request.urlopen(req, timeout=30) as resp: - Network accessline 69
with urllib.request.urlopen(req, timeout=30) as resp:
skills/clinical-trial-finder/opentargets.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 4
GraphQL endpoint: https://api.platform.opentargets.org/api/v4/graphql - Network accessline 4
GraphQL endpoint: https://api.platform.opentargets.org/api/v4/graphql - Network accessline 18
OT_GRAPHQL = "https://api.platform.opentargets.org/api/v4/graphql" - Network accessline 18
OT_GRAPHQL = "https://api.platform.opentargets.org/api/v4/graphql" - Network accessline 92
payload = json.dumps({"query": query, "variables": variables}).encode() req = urllib.request.Request( - Network accessline 92
payload = json.dumps({"query": query, "variables": variables}).encode() req = urllib.request.Request( - Network accessline 93
req = urllib.request.Request( - Network accessline 93
req = urllib.request.Request( - Network accessline 98
) try: with urllib.request.urlopen(req, timeout=15) as resp: - Network accessline 98
) try: with urllib.request.urlopen(req, timeout=15) as resp: - Network accessline 99
try: with urllib.request.urlopen(req, timeout=15) as resp: result = json.loads(resp.read().decode()) - Network accessline 99
try: with urllib.request.urlopen(req, timeout=15) as resp: result = json.loads(resp.read().decode()) - Network accessline 100
with urllib.request.urlopen(req, timeout=15) as resp: - Network accessline 100
with urllib.request.urlopen(req, timeout=15) as resp:
skills/clinical-trial-finder/tests/test_clinical_trial_finder.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 153
def test_fetch_trials_network_error(): with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 153
def test_fetch_trials_network_error(): with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 154
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 154
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("timeout")): - Network accessline 162
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = b"not-json{" with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 162
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = b"not-json{" with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 163
mock_resp.read.return_value = b"not-json{" with patch("urllib.request.urlopen", return_value=mock_resp): with pytest.raises(RuntimeError, match="malformed JSON"): - Network accessline 163
mock_resp.read.return_value = b"not-json{" with patch("urllib.request.urlopen", return_value=mock_resp): with pytest.raises(RuntimeError, match="malformed JSON"): - Network accessline 164
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 164
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 172
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = json.dumps({"studies": []}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 172
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = json.dumps({"studies": []}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 173
mock_resp.read.return_value = json.dumps({"studies": []}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): result = api.fetch_trials("nothing-matches-this-query-xyz") - Network accessline 173
mock_resp.read.return_value = json.dumps({"studies": []}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): result = api.fetch_trials("nothing-matches-this-query-xyz") - Network accessline 174
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 174
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 352
cond = bundle["entry"][0]["resource"]["condition"][0] assert "coding" in cond assert cond["coding"][0]["system"] == "http://id.nlm.nih.gov/mesh/" - Network accessline 352
cond = bundle["entry"][0]["resource"]["condition"][0] assert "coding" in cond assert cond["coding"][0]["system"] == "http://id.nlm.nih.gov/mesh/" - Network accessline 353
assert "coding" in cond assert cond["coding"][0]["system"] == "http://id.nlm.nih.gov/mesh/" assert cond["coding"][0]["code"] == "D001943" - Network accessline 353
assert "coding" in cond assert cond["coding"][0]["system"] == "http://id.nlm.nih.gov/mesh/" assert cond["coding"][0]["code"] == "D001943" - Network accessline 354
assert cond["coding"][0]["system"] == "http://id.nlm.nih.gov/mesh/" - Network accessline 354
assert cond["coding"][0]["system"] == "http://id.nlm.nih.gov/mesh/" - Network accessline 451
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 451
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 452
) with patch("urllib.request.urlopen", return_value=resp): ensembl_id, name = ot.resolve_gene("BRCA1") - Network accessline 452
) with patch("urllib.request.urlopen", return_value=resp): ensembl_id, name = ot.resolve_gene("BRCA1") - Network accessline 453
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 453
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 459
def test_ot_resolve_gene_not_found(): resp = _make_ot_response({"search": {"hits": []}}) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 459
def test_ot_resolve_gene_not_found(): resp = _make_ot_response({"search": {"hits": []}}) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 460
resp = _make_ot_response({"search": {"hits": []}}) with patch("urllib.request.urlopen", return_value=resp): with pytest.raises(ValueError, match="not found"): - Network accessline 460
resp = _make_ot_response({"search": {"hits": []}}) with patch("urllib.request.urlopen", return_value=resp): with pytest.raises(ValueError, match="not found"): - Network accessline 461
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 461
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 487
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 487
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 488
) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048", min_score=0.6) - Network accessline 488
) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048", min_score=0.6) - Network accessline 489
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 489
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 497
def test_ot_network_error(): with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("refused")): - Network accessline 497
def test_ot_network_error(): with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("refused")): - Network accessline 498
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("refused")): - Network accessline 498
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("refused")): - Network accessline 508
{"errors": [{"message": "Field not found"}]} ).encode() with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 508
{"errors": [{"message": "Field not found"}]} ).encode() with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 509
).encode() with patch("urllib.request.urlopen", return_value=mock_resp): with pytest.raises(RuntimeError, match="GraphQL error"): - Network accessline 509
).encode() with patch("urllib.request.urlopen", return_value=mock_resp): with pytest.raises(RuntimeError, match="GraphQL error"): - Network accessline 510
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 510
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 656
with patch("urllib.request.urlopen", side_effect=mock_urlopen): - Network accessline 656
with patch("urllib.request.urlopen", side_effect=mock_urlopen): - Network accessline 673
with patch("urllib.request.urlopen", side_effect=mock_urlopen): - Network accessline 673
with patch("urllib.request.urlopen", side_effect=mock_urlopen): - Network accessline 782
content = (tmp_path / "report.md").read_text() for t in MOCK_TRIALS: assert f"https://clinicaltrials.gov/study/{t['nct_id']}" in content - Network accessline 782
content = (tmp_path / "report.md").read_text() for t in MOCK_TRIALS: assert f"https://clinicaltrials.gov/study/{t['nct_id']}" in content - Network accessline 784
assert f"https://clinicaltrials.gov/study/{t['nct_id']}" in content - Network accessline 784
assert f"https://clinicaltrials.gov/study/{t['nct_id']}" in content - Network accessline 849
bundle = json.loads(path.read_text()) entry = bundle["entry"][0] assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" - Network accessline 849
bundle = json.loads(path.read_text()) entry = bundle["entry"][0] assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" - Network accessline 851
assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" - Network accessline 851
assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" - Network accessline 870
prefixed = {**euctr_trial, "nct_id": "EUCTR2024-000001-12"} expected = ( "https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 870
prefixed = {**euctr_trial, "nct_id": "EUCTR2024-000001-12"} expected = ( "https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 871
expected = ( "https://www.clinicaltrialsregister.eu/ctr-search/search" "?query=2024-000001-12" - Network accessline 871
expected = ( "https://www.clinicaltrialsregister.eu/ctr-search/search" "?query=2024-000001-12" - Network accessline 872
"https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 872
"https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 877
report_text = report.read_text() assert expected in report_text assert "https://clinicaltrials.gov/study/2024-000001-12" not in report_text - Network accessline 877
report_text = report.read_text() assert expected in report_text assert "https://clinicaltrials.gov/study/2024-000001-12" not in report_text - Network accessline 878
assert expected in report_text assert "https://clinicaltrials.gov/study/2024-000001-12" not in report_text assert "**EudraCT ID**" in report_text - Network accessline 878
assert expected in report_text assert "https://clinicaltrials.gov/study/2024-000001-12" not in report_text assert "**EudraCT ID**" in report_text - Network accessline 879
assert "https://clinicaltrials.gov/study/2024-000001-12" not in report_text - Network accessline 879
assert "https://clinicaltrials.gov/study/2024-000001-12" not in report_text - Network accessline 882
html = wr.write_html({"query": "rare disease"}, [euctr_trial], tmp_path).read_text() assert expected in html assert "https://clinicaltrials.gov/study/2024-000001-12" not in html - Network accessline 882
html = wr.write_html({"query": "rare disease"}, [euctr_trial], tmp_path).read_text() assert expected in html assert "https://clinicaltrials.gov/study/2024-000001-12" not in html - Network accessline 884
assert "https://clinicaltrials.gov/study/2024-000001-12" not in html - Network accessline 884
assert "https://clinicaltrials.gov/study/2024-000001-12" not in html - Network accessline 886
entry = json.loads(wr.write_fhir_bundle([euctr_trial], tmp_path).read_text())["entry"][0] assert entry["fullUrl"] == expected assert entry["resource"]["identifier"][0]["system"] == "https://www.clinicaltrialsregister.eu" - Network accessline 886
entry = json.loads(wr.write_fhir_bundle([euctr_trial], tmp_path).read_text())["entry"][0] assert entry["fullUrl"] == expected assert entry["resource"]["identifier"][0]["system"] == "https://www.clinicaltrialsregister.eu" - Network accessline 887
assert entry["fullUrl"] == expected assert entry["resource"]["identifier"][0]["system"] == "https://www.clinicaltrialsregister.eu" assert entry["resource"]["identifier"][0]["value"] == "2024-000001-12" - Network accessline 887
assert entry["fullUrl"] == expected assert entry["resource"]["identifier"][0]["system"] == "https://www.clinicaltrialsregister.eu" assert entry["resource"]["identifier"][0]["value"] == "2024-000001-12" - Network accessline 888
assert entry["resource"]["identifier"][0]["system"] == "https://www.clinicaltrialsregister.eu" - Network accessline 888
assert entry["resource"]["identifier"][0]["system"] == "https://www.clinicaltrialsregister.eu" - Network accessline 899
ctgov = {**MOCK_TRIALS[0], "source": "clinicaltrials.gov"} report = wr.write_report(MOCK_QUERY, [ctgov], tmp_path).read_text() assert "https://clinicaltrials.gov/study/NCT00000001" in report - Network accessline 899
ctgov = {**MOCK_TRIALS[0], "source": "clinicaltrials.gov"} report = wr.write_report(MOCK_QUERY, [ctgov], tmp_path).read_text() assert "https://clinicaltrials.gov/study/NCT00000001" in report - Network accessline 900
report = wr.write_report(MOCK_QUERY, [ctgov], tmp_path).read_text() assert "https://clinicaltrials.gov/study/NCT00000001" in report entry = json.loads(wr.write_fhir_bundle([ctgov], tmp_path).read_text())["entry"][0] - Network accessline 900
report = wr.write_report(MOCK_QUERY, [ctgov], tmp_path).read_text() assert "https://clinicaltrials.gov/study/NCT00000001" in report entry = json.loads(wr.write_fhir_bundle([ctgov], tmp_path).read_text())["entry"][0] - Network accessline 901
assert "https://clinicaltrials.gov/study/NCT00000001" in report - Network accessline 901
assert "https://clinicaltrials.gov/study/NCT00000001" in report - Network accessline 902
entry = json.loads(wr.write_fhir_bundle([ctgov], tmp_path).read_text())["entry"][0] assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" assert entry["resource"]["identifier"][0]["system"] == "https://clinicaltr - Network accessline 902
entry = json.loads(wr.write_fhir_bundle([ctgov], tmp_path).read_text())["entry"][0] assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" assert entry["resource"]["identifier"][0]["system"] == "https://clinicaltr - Network accessline 903
assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" - Network accessline 903
assert entry["fullUrl"] == "https://clinicaltrials.gov/study/NCT00000001" - Network accessline 904
assert entry["resource"]["identifier"][0]["system"] == "https://clinicaltrials.gov" - Network accessline 904
assert entry["resource"]["identifier"][0]["system"] == "https://clinicaltrials.gov" - Network accessline 1073
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("refused")): - Network accessline 1073
with patch("urllib.request.urlopen", side_effect=urllib.error.URLError("refused")): - Network accessline 1174
wr.write_html(MOCK_QUERY, MOCK_TRIALS, tmp_path) content = (tmp_path / "report.html").read_text() assert "https://clinicaltrials.gov/study/NCT00000001" in content - Network accessline 1174
wr.write_html(MOCK_QUERY, MOCK_TRIALS, tmp_path) content = (tmp_path / "report.html").read_text() assert "https://clinicaltrials.gov/study/NCT00000001" in content - Network accessline 1176
assert "https://clinicaltrials.gov/study/NCT00000001" in content - Network accessline 1176
assert "https://clinicaltrials.gov/study/NCT00000001" in content - Network accessline 1255
"entry": [ { "fullUrl": "https://example.com", - Network accessline 1255
"entry": [ { "fullUrl": "https://example.com", - Network accessline 1256
{ "fullUrl": "https://example.com", "resource": { - Network accessline 1256
{ "fullUrl": "https://example.com", "resource": { - Network accessline 1257
"fullUrl": "https://example.com", - Network accessline 1257
"fullUrl": "https://example.com", - Network accessline 1279
"entry": [ { "fullUrl": "https://example.com", - Network accessline 1279
"entry": [ { "fullUrl": "https://example.com", - Network accessline 1280
{ "fullUrl": "https://example.com", "resource": { - Network accessline 1280
{ "fullUrl": "https://example.com", "resource": { - Network accessline 1281
"fullUrl": "https://example.com", - Network accessline 1281
"fullUrl": "https://example.com", - Network accessline 1373
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1373
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1374
) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048", min_score=0.5, max_results=3) - Network accessline 1374
) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048", min_score=0.5, max_results=3) - Network accessline 1375
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1375
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1380
def test_ot_get_diseases_empty_rows(): resp = _make_ot_response({"target": {"associatedDiseases": {"rows": []}}}) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1380
def test_ot_get_diseases_empty_rows(): resp = _make_ot_response({"target": {"associatedDiseases": {"rows": []}}}) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1381
resp = _make_ot_response({"target": {"associatedDiseases": {"rows": []}}}) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048") - Network accessline 1381
resp = _make_ot_response({"target": {"associatedDiseases": {"rows": []}}}) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048") - Network accessline 1382
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1382
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1398
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1398
} ) with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1399
) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048", min_score=0.6) - Network accessline 1399
) with patch("urllib.request.urlopen", return_value=resp): diseases = ot.get_diseases("ENSG00000012048", min_score=0.6) - Network accessline 1400
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1400
with patch("urllib.request.urlopen", return_value=resp): - Network accessline 1415
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = b"not json at all" with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1415
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = b"not json at all" with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1416
mock_resp.read.return_value = b"not json at all" with patch("urllib.request.urlopen", return_value=mock_resp): with pytest.raises(RuntimeError, match="malformed JSON"): - Network accessline 1416
mock_resp.read.return_value = b"not json at all" with patch("urllib.request.urlopen", return_value=mock_resp): with pytest.raises(RuntimeError, match="malformed JSON"): - Network accessline 1417
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1417
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1510
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = json.dumps({"studies": [raw_study]}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1510
mock_resp.__exit__ = MagicMock(return_value=False) mock_resp.read.return_value = json.dumps({"studies": [raw_study]}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1511
mock_resp.read.return_value = json.dumps({"studies": [raw_study]}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): trials = api.fetch_trials("test") - Network accessline 1511
mock_resp.read.return_value = json.dumps({"studies": [raw_study]}).encode() with patch("urllib.request.urlopen", return_value=mock_resp): trials = api.fetch_trials("test") - Network accessline 1512
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1512
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1530
bundle = json.loads(path.read_text()) assert "meta" in bundle assert bundle["meta"]["tag"][0]["system"] == "https://clawbio.ai" - Network accessline 1530
bundle = json.loads(path.read_text()) assert "meta" in bundle assert bundle["meta"]["tag"][0]["system"] == "https://clawbio.ai" - Network accessline 1531
assert "meta" in bundle assert bundle["meta"]["tag"][0]["system"] == "https://clawbio.ai" assert bundle["meta"]["tag"][0]["code"] == "clinical-trial-finder" - Network accessline 1531
assert "meta" in bundle assert bundle["meta"]["tag"][0]["system"] == "https://clawbio.ai" assert bundle["meta"]["tag"][0]["code"] == "clinical-trial-finder" - Network accessline 1532
assert bundle["meta"]["tag"][0]["system"] == "https://clawbio.ai" - Network accessline 1532
assert bundle["meta"]["tag"][0]["system"] == "https://clawbio.ai" - Network accessline 1540
assert "meta" in resource assert ( "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 1540
assert "meta" in resource assert ( "http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 1541
assert ( "http://hl7.org/fhir/StructureDefinition/ResearchStudy" in resource["meta"]["profile"] - Network accessline 1541
assert ( "http://hl7.org/fhir/StructureDefinition/ResearchStudy" in resource["meta"]["profile"] - Network accessline 1542
"http://hl7.org/fhir/StructureDefinition/ResearchStudy" - Network accessline 1542
"http://hl7.org/fhir/StructureDefinition/ResearchStudy"
skills/clinical-trial-finder/tests/test_fhir_e2e.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 41
# FHIR R4 dateTime regex — accepts YYYY, YYYY-MM, YYYY-MM-DD, or full datetime # Source: https://hl7.org/fhir/R4/datatypes.html#dateTime - Network accessline 41
# FHIR R4 dateTime regex — accepts YYYY, YYYY-MM, YYYY-MM-DD, or full datetime # Source: https://hl7.org/fhir/R4/datatypes.html#dateTime - Network accessline 42
# Source: https://hl7.org/fhir/R4/datatypes.html#dateTime - Network accessline 42
# Source: https://hl7.org/fhir/R4/datatypes.html#dateTime - Network accessline 87
PHASE_SYSTEM = "http://terminology.hl7.org/CodeSystem/research-study-phase" - Network accessline 87
PHASE_SYSTEM = "http://terminology.hl7.org/CodeSystem/research-study-phase"
skills/clinical-trial-finder/tests/test_gwas_bridge_v2.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 65
def test_api_base_is_v2(): assert gwas_bridge._GWAS_API == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 65
def test_api_base_is_v2(): assert gwas_bridge._GWAS_API == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 66
assert gwas_bridge._GWAS_API == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 66
assert gwas_bridge._GWAS_API == "https://www.ebi.ac.uk/gwas/rest/api/v2"
skills/clinical-trial-finder/writers.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 69
query = urllib.parse.quote(_euctr_registry_id(identifier), safe="") return ( "https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 69
query = urllib.parse.quote(_euctr_registry_id(identifier), safe="") return ( "https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 70
return ( "https://www.clinicaltrialsregister.eu/ctr-search/search" f"?query={query}" - Network accessline 70
return ( "https://www.clinicaltrialsregister.eu/ctr-search/search" f"?query={query}" - Network accessline 71
"https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 71
"https://www.clinicaltrialsregister.eu/ctr-search/search" - Network accessline 72
f"?query={query}" ) return f"https://clinicaltrials.gov/study/{identifier}" - Network accessline 72
f"?query={query}" ) return f"https://clinicaltrials.gov/study/{identifier}" - Network accessline 74
return f"https://clinicaltrials.gov/study/{identifier}" - Network accessline 74
return f"https://clinicaltrials.gov/study/{identifier}" - Network accessline 77
def _trial_identifier_system(trial: dict) -> str: if trial.get("source") == "euctr": return "https://www.clinicaltrialsregister.eu" - Network accessline 77
def _trial_identifier_system(trial: dict) -> str: if trial.get("source") == "euctr": return "https://www.clinicaltrialsregister.eu" - Network accessline 78
if trial.get("source") == "euctr": return "https://www.clinicaltrialsregister.eu" return "https://clinicaltrials.gov" - Network accessline 78
if trial.get("source") == "euctr": return "https://www.clinicaltrialsregister.eu" return "https://clinicaltrials.gov" - Network accessline 79
return "https://www.clinicaltrialsregister.eu" - Network accessline 79
return "https://www.clinicaltrialsregister.eu" - Network accessline 80
return "https://clinicaltrials.gov" - Network accessline 80
return "https://clinicaltrials.gov" - Network accessline 225
"entry": entries, "meta": { "tag": [{"system": "https://clawbio.ai", "code": "clinical-trial-finder"}] - Network accessline 225
"entry": entries, "meta": { "tag": [{"system": "https://clawbio.ai", "code": "clinical-trial-finder"}] - Network accessline 226
"meta": { "tag": [{"system": "https://clawbio.ai", "code": "clinical-trial-finder"}] }, - Network accessline 226
"meta": { "tag": [{"system": "https://clawbio.ai", "code": "clinical-trial-finder"}] }, - Network accessline 227
"tag": [{"system": "https://clawbio.ai", "code": "clinical-trial-finder"}] - Network accessline 227
"tag": [{"system": "https://clawbio.ai", "code": "clinical-trial-finder"}] - Network accessline 249
"resourceType": "ResearchStudy", "id": t["nct_id"], "meta": {"profile": ["http://hl7.org/fhir/StructureDefinition/ResearchStudy"]}, - Network accessline 249
"resourceType": "ResearchStudy", "id": t["nct_id"], "meta": {"profile": ["http://hl7.org/fhir/StructureDefinition/ResearchStudy"]}, - Network accessline 250
"id": t["nct_id"], "meta": {"profile": ["http://hl7.org/fhir/StructureDefinition/ResearchStudy"]}, "identifier": [ - Network accessline 250
"id": t["nct_id"], "meta": {"profile": ["http://hl7.org/fhir/StructureDefinition/ResearchStudy"]}, "identifier": [ - Network accessline 251
"meta": {"profile": ["http://hl7.org/fhir/StructureDefinition/ResearchStudy"]}, - Network accessline 251
"meta": {"profile": ["http://hl7.org/fhir/StructureDefinition/ResearchStudy"]}, - Network accessline 268
k: v for k, v in { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 268
k: v for k, v in { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 269
for k, v in { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", "code": FHIR_PHASE.get(t["phase"], "n-a"), - Network accessline 269
for k, v in { "system": "http://terminology.hl7.org/CodeSystem/research-study-phase", "code": FHIR_PHASE.get(t["phase"], "n-a"), - Network accessline 270
"system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 270
"system": "http://terminology.hl7.org/CodeSystem/research-study-phase", - Network accessline 284
"coding": [ { "system": "http://clinicaltrials.gov/study-type", - Network accessline 284
"coding": [ { "system": "http://clinicaltrials.gov/study-type", - Network accessline 285
{ "system": "http://clinicaltrials.gov/study-type", "code": t["study_type"], - Network accessline 285
{ "system": "http://clinicaltrials.gov/study-type", "code": t["study_type"], - Network accessline 286
"system": "http://clinicaltrials.gov/study-type", - Network accessline 286
"system": "http://clinicaltrials.gov/study-type", - Network accessline 299
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 299
"coding": [ { "system": "http://id.nlm.nih.gov/mesh/", - Network accessline 300
{ "system": "http://id.nlm.nih.gov/mesh/", "code": m["id"], - Network accessline 300
{ "system": "http://id.nlm.nih.gov/mesh/", "code": m["id"], - Network accessline 301
"system": "http://id.nlm.nih.gov/mesh/", - Network accessline 301
"system": "http://id.nlm.nih.gov/mesh/",
skills/clinical-variant-prioritizer/api.py
skills/clinical-variant-prioritizer/prioritize.py
skills/clinical-variant-prioritizer/tests/test_api.py
skills/clinical-variant-reporter/SKILL.md
- Network accessline 23
always: false emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
always: false emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio - Network accessline 24
emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 253
- [Richards et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/25741868/) — ACMG/AMP standards and guidelines for the interpretation of sequence variants. *Genet Med* 17:405–424 - Network accessline 253
- [Richards et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/25741868/) — ACMG/AMP standards and guidelines for the interpretation of sequence variants. *Genet Med* 17:405–424 - Network accessline 254
- [Rehm et al. (2013)](https://pubmed.ncbi.nlm.nih.gov/23887774/) — ACMG clinical laboratory standards for next-generation sequencing. *Genet Med* 15:733–747 - Network accessline 254
- [Rehm et al. (2013)](https://pubmed.ncbi.nlm.nih.gov/23887774/) — ACMG clinical laboratory standards for next-generation sequencing. *Genet Med* 15:733–747 - Network accessline 255
- [Miller et al. (2023)](https://pmc.ncbi.nlm.nih.gov/articles/PMC10524344/) — ACMG SF v3.2 list for reporting of secondary findings. *Genet Med* 25:100866 - Network accessline 255
- [Miller et al. (2023)](https://pmc.ncbi.nlm.nih.gov/articles/PMC10524344/) — ACMG SF v3.2 list for reporting of secondary findings. *Genet Med* 25:100866 - Network accessline 256
- [Abou Tayoun et al. (2018)](https://pubmed.ncbi.nlm.nih.gov/30192042/) — PVS1 ACMG/AMP variant criterion recommendations. *Human Mutation* 39:1517–1524 - Network accessline 256
- [Abou Tayoun et al. (2018)](https://pubmed.ncbi.nlm.nih.gov/30192042/) — PVS1 ACMG/AMP variant criterion recommendations. *Human Mutation* 39:1517–1524 - Network accessline 257
- [Li & Wang (2017)](https://pubmed.ncbi.nlm.nih.gov/28132688/) — InterVar: clinical interpretation of genetic variants. *Am J Hum Genet* 100:267–280 - Network accessline 257
- [Li & Wang (2017)](https://pubmed.ncbi.nlm.nih.gov/28132688/) — InterVar: clinical interpretation of genetic variants. *Am J Hum Genet* 100:267–280 - Network accessline 258
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) — NCBI clinical significance database - Network accessline 258
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) — NCBI clinical significance database - Network accessline 259
- [gnomAD](https://gnomad.broadinstitute.org/) — Genome Aggregation Database - Network accessline 259
- [gnomAD](https://gnomad.broadinstitute.org/) — Genome Aggregation Database - Network accessline 260
- [ClinGen](https://clinicalgenome.org/) — Clinical Genome Resource - Network accessline 260
- [ClinGen](https://clinicalgenome.org/) — Clinical Genome Resource
skills/clinical-variant-reporter/acmg_engine.py
skills/clinical-variant-reporter/clinical_variant_reporter.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 46
VEP_REST_HOST = "https://rest.ensembl.org" - Network accessline 46
VEP_REST_HOST = "https://rest.ensembl.org" - Network accessline 47
VEP_REST_HOST_GRCH37 = "https://grch37.rest.ensembl.org" - Network accessline 47
VEP_REST_HOST_GRCH37 = "https://grch37.rest.ensembl.org" - Network accessline 334
try: import requests resp = requests.get( - Network accessline 334
try: import requests resp = requests.get( - Network accessline 335
import requests resp = requests.get( _ensembl_rest_host(assembly) + ENSEMBL_INFO_VARIATION_PATH, - Network accessline 335
import requests resp = requests.get( _ensembl_rest_host(assembly) + ENSEMBL_INFO_VARIATION_PATH, - Network accessline 336
resp = requests.get( - Network accessline 336
resp = requests.get( - Network accessline 390
try: resp = requests.post( - Network accessline 390
try: resp = requests.post( - Network accessline 391
resp = requests.post( - Network accessline 391
resp = requests.post(
skills/clinical-variant-reporter/self_audit.py
skills/clinical-variant-reporter/tests/__init__.py
skills/clinical-variant-reporter/tests/test_clinical_variant_reporter.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 763
assert len(captured_args) == 1 called_url = captured_args[0][0] if captured_args[0] else captured_kwargs[0].get("url") assert called_url == "https://rest.ensembl.org/info/variation/homo_sapiens" - Network accessline 763
assert len(captured_args) == 1 called_url = captured_args[0][0] if captured_args[0] else captured_kwargs[0].get("url") assert called_url == "https://rest.ensembl.org/info/variation/homo_sapiens" - Network accessline 764
called_url = captured_args[0][0] if captured_args[0] else captured_kwargs[0].get("url") assert called_url == "https://rest.ensembl.org/info/variation/homo_sapiens" assert called_url == VEP_REST_HOST + ENSEMBL_INFO_VARIATION_ - Network accessline 764
called_url = captured_args[0][0] if captured_args[0] else captured_kwargs[0].get("url") assert called_url == "https://rest.ensembl.org/info/variation/homo_sapiens" assert called_url == VEP_REST_HOST + ENSEMBL_INFO_VARIATION_ - Network accessline 765
assert called_url == "https://rest.ensembl.org/info/variation/homo_sapiens" - Network accessline 765
assert called_url == "https://rest.ensembl.org/info/variation/homo_sapiens" - Network accessline 1001
object whose raise_for_status() genuinely raises for a 4xx/5xx status, driving the real code path rather than short-circuiting at requests.get() itself.""" - Network accessline 1001
object whose raise_for_status() genuinely raises for a 4xx/5xx status, driving the real code path rather than short-circuiting at requests.get() itself.""" - Network accessline 1003
requests.get() itself.""" - Network accessline 1003
requests.get() itself."""
skills/clinical-variant-reporter/tests/test_self_audit.py
skills/clinpgx/SKILL.md
- Network accessline 12
always: false emoji: 🧬 homepage: https://api.clinpgx.org/ - Network accessline 12
always: false emoji: 🧬 homepage: https://api.clinpgx.org/ - Network accessline 13
emoji: 🧬 homepage: https://api.clinpgx.org/ os: - Network accessline 13
emoji: 🧬 homepage: https://api.clinpgx.org/ os: - Network accessline 14
homepage: https://api.clinpgx.org/ - Network accessline 14
homepage: https://api.clinpgx.org/ - Network accessline 26
You are **ClinPGx**, a specialised ClawBio agent for querying the ClinPGx pharmacogenomics database. Your role is to look up gene-drug interactions, clinical annotations, CPIC guidelines, FDA drug labels, and allele definitions from the Cli - Network accessline 26
You are **ClinPGx**, a specialised ClawBio agent for querying the ClinPGx pharmacogenomics database. Your role is to look up gene-drug interactions, clinical annotations, CPIC guidelines, FDA drug labels, and allele definitions from the Cli
skills/clinpgx/clinpgx.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 41
BASE_URL = "https://api.clinpgx.org/v1" RATE_LIMIT_INTERVAL = 0.55 # seconds between requests (stay under 2 req/sec) - Network accessline 41
BASE_URL = "https://api.clinpgx.org/v1" RATE_LIMIT_INTERVAL = 0.55 # seconds between requests (stay under 2 req/sec) - Network accessline 63
self.use_cache = use_cache self._last_request_time = 0.0 self.session = requests.Session() - Network accessline 63
self.use_cache = use_cache self._last_request_time = 0.0 self.session = requests.Session() - Network accessline 64
self._last_request_time = 0.0 self.session = requests.Session() self.session.headers.update({ - Network accessline 64
self._last_request_time = 0.0 self.session = requests.Session() self.session.headers.update({ - Network accessline 65
self.session = requests.Session() - Network accessline 65
self.session = requests.Session()
skills/clinpgx/tests/__init__.py
skills/clinpgx/tests/test_clinpgx.py
skills/cnv-acmg-classifier/SKILL.md
- Network accessline 67
always: false emoji: "🦖" homepage: https://github.com/ClawBio/ClawBio - Network accessline 67
always: false emoji: "🦖" homepage: https://github.com/ClawBio/ClawBio - Network accessline 68
emoji: "🦖" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 68
emoji: "🦖" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 69
homepage: https://github.com/ClawBio/ClawBio - Network accessline 69
homepage: https://github.com/ClawBio/ClawBio - Network accessline 255
- [Riggs ER et al., Genet Med 2020 (ClinGen/ACMG technical standards for CNV interpretation)](https://pubmed.ncbi.nlm.nih.gov/31690835/); the point framework and thresholds. - Network accessline 255
- [Riggs ER et al., Genet Med 2020 (ClinGen/ACMG technical standards for CNV interpretation)](https://pubmed.ncbi.nlm.nih.gov/31690835/); the point framework and thresholds. - Network accessline 256
- [ClinGen Dosage Sensitivity Map](https://dosage.clinicalgenome.org/); established haploinsufficiency / triplosensitivity calls. - Network accessline 256
- [ClinGen Dosage Sensitivity Map](https://dosage.clinicalgenome.org/); established haploinsufficiency / triplosensitivity calls.
skills/cnv-acmg-classifier/cnv_acmg_classifier.py
skills/cnv-acmg-classifier/tests/test_cnv_acmg_classifier.py
skills/crispr-screen-triage/SKILL.md
- Network accessline 43
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 43
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 44
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 44
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 45
homepage: https://github.com/ClawBio/ClawBio - Network accessline 45
homepage: https://github.com/ClawBio/ClawBio
skills/crispr-screen-triage/crispr_screen_triage.py
skills/crispr-screen-triage/tests/test_crispr_screen_triage.py
skills/data-extractor/SKILL.md
- Access to secretsline 13
[Credential-related source omitted] - Access to secretsline 13
[Credential-related source omitted] - Network accessline 14
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 15
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 15
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 16
homepage: https://github.com/ClawBio/ClawBio - Network accessline 16
homepage: https://github.com/ClawBio/ClawBio - Access to secretsline 92
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted]
skills/data-extractor/data_extractor.py
skills/data-extractor/data_extractor_api.py
skills/data-extractor/data_extractor_core/__init__.py
skills/data-extractor/data_extractor_core/cv_calibration.py
skills/data-extractor/data_extractor_core/digitizer.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Possible obfuscationline 930
return Image.open(io.BytesIO(base64.b64decode(b64))) - Possible obfuscationline 930
return Image.open(io.BytesIO(base64.b64decode(b64))) - Possible obfuscationline 1163
img_bytes = base64.b64decode(figure.image_base64) - Possible obfuscationline 1163
img_bytes = base64.b64decode(figure.image_base64)
skills/data-extractor/data_extractor_core/models.py
skills/data-extractor/tests/test_extractor.py
skills/data-extractor/web/app.js
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 20
async function api(url, options) { options = options || {}; var resp = await fetch(url, { - Network accessline 20
async function api(url, options) { options = options || {}; var resp = await fetch(url, { - Network accessline 21
options = options || {}; var resp = await fetch(url, { headers: { "Content-Type": "application/json" }, - Network accessline 21
options = options || {}; var resp = await fetch(url, { headers: { "Content-Type": "application/json" }, - Network accessline 22
var resp = await fetch(url, { - Network accessline 22
var resp = await fetch(url, { - Network accessline 38
formData.append("file", file); try { var resp = await fetch("/api/upload-image", { method: "POST", body: formData }); - Network accessline 38
formData.append("file", file); try { var resp = await fetch("/api/upload-image", { method: "POST", body: formData }); - Network accessline 39
try { var resp = await fetch("/api/upload-image", { method: "POST", body: formData }); if (!resp.ok) { - Network accessline 39
try { var resp = await fetch("/api/upload-image", { method: "POST", body: formData }); if (!resp.ok) { - Network accessline 40
var resp = await fetch("/api/upload-image", { method: "POST", body: formData }); - Network accessline 40
var resp = await fetch("/api/upload-image", { method: "POST", body: formData }); - Network accessline 65
async function loadExample(name) { try { var resp = await fetch("/static/examples/" + name + ".png"); - Network accessline 65
async function loadExample(name) { try { var resp = await fetch("/static/examples/" + name + ".png"); - Network accessline 66
try { var resp = await fetch("/static/examples/" + name + ".png"); if (!resp.ok) throw new Error("Example not found"); - Network accessline 66
try { var resp = await fetch("/static/examples/" + name + ".png"); if (!resp.ok) throw new Error("Example not found"); - Network accessline 67
var resp = await fetch("/static/examples/" + name + ".png"); - Network accessline 67
var resp = await fetch("/static/examples/" + name + ".png"); - Network accessline 517
if (currentImageId && field) { fetch("/api/edit-cell", { - Network accessline 517
if (currentImageId && field) { fetch("/api/edit-cell", { - Network accessline 518
fetch("/api/edit-cell", { - Network accessline 518
fetch("/api/edit-cell", { - Network accessline 727
var parts = []; parts.push('<svg width="' + W + '" height="' + H + '" viewBox="0 0 ' + W + ' ' + H + '" xmlns="http://www.w3.org/2000/svg" style="max-width:100%">'); - Network accessline 727
var parts = []; parts.push('<svg width="' + W + '" height="' + H + '" viewBox="0 0 ' + W + ' ' + H + '" xmlns="http://www.w3.org/2000/svg" style="max-width:100%">'); - Network accessline 728
parts.push('<svg width="' + W + '" height="' + H + '" viewBox="0 0 ' + W + ' ' + H + '" xmlns="http://www.w3.org/2000/svg" style="max-width:100%">'); - Network accessline 728
parts.push('<svg width="' + W + '" height="' + H + '" viewBox="0 0 ' + W + ' ' + H + '" xmlns="http://www.w3.org/2000/svg" style="max-width:100%">');
skills/data-extractor/web/index.html
- Network accessline 5
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Get Me The Data</title> <script src="https://cdn.tailwindcss.com"></script> - Network accessline 5
<meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Get Me The Data</title> <script src="https://cdn.tailwindcss.com"></script> - Network accessline 6
<title>Get Me The Data</title> <script src="https://cdn.tailwindcss.com"></script> <link rel="stylesheet" href="styles.css"> - Network accessline 6
<title>Get Me The Data</title> <script src="https://cdn.tailwindcss.com"></script> <link rel="stylesheet" href="styles.css"> - Network accessline 7
<script src="https://cdn.tailwindcss.com"></script> - Network accessline 7
<script src="https://cdn.tailwindcss.com"></script> - Network accessline 18
</div> <div class="flex items-center gap-2 text-sm text-gray-400"> <svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg"> - Network accessline 18
</div> <div class="flex items-center gap-2 text-sm text-gray-400"> <svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg"> - Network accessline 19
<div class="flex items-center gap-2 text-sm text-gray-400"> <svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg"> <path d="M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 - Network accessline 19
<div class="flex items-center gap-2 text-sm text-gray-400"> <svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg"> <path d="M12 2C6.48 2 2 6.48 2 12s4.48 10 10 10 - Network accessline 20
<svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg"> - Network accessline 20
<svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg">
skills/data-extractor/web/server.py
skills/de-summary/SKILL.md
- Network accessline 39
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 39
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 40
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 40
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 41
homepage: https://github.com/ClawBio/ClawBio - Network accessline 41
homepage: https://github.com/ClawBio/ClawBio
skills/deepspot-m/SKILL.md
- Network accessline 68
always: false emoji: "🧬" homepage: https://github.com/ratschlab/DeepSpotM - Network accessline 68
always: false emoji: "🧬" homepage: https://github.com/ratschlab/DeepSpotM - Network accessline 69
emoji: "🧬" homepage: https://github.com/ratschlab/DeepSpotM os: - Network accessline 69
emoji: "🧬" homepage: https://github.com/ratschlab/DeepSpotM os: - Network accessline 70
homepage: https://github.com/ratschlab/DeepSpotM - Network accessline 70
homepage: https://github.com/ratschlab/DeepSpotM - Network accessline 327
**Licensing and access**, stated plainly because it decides whether you may use this: - This skill's own wrapper code is MIT. That grants nothing over the weights; the fields below are the ones that restrict you. - Upstream code is [PolyFor - Network accessline 327
**Licensing and access**, stated plainly because it decides whether you may use this: - This skill's own wrapper code is MIT. That grants nothing over the weights; the fields below are the ones that restrict you. - Upstream code is [PolyFor - Network accessline 328
- This skill's own wrapper code is MIT. That grants nothing over the weights; the fields below are the ones that restrict you. - Upstream code is [PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0/). Non - Network accessline 328
- This skill's own wrapper code is MIT. That grants nothing over the weights; the fields below are the ones that restrict you. - Upstream code is [PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0/). Non - Network accessline 329
- Upstream code is [PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0/). Non-commercial use only. You install `deepspotm` yourself and accept that directly; nothing from upstream is vendored here. - Mode - Network accessline 329
- Upstream code is [PolyForm Noncommercial 1.0.0](https://polyformproject.org/licenses/noncommercial/1.0.0/). Non-commercial use only. You install `deepspotm` yourself and accept that directly; nothing from upstream is vendored here. - Mode - Network accessline 354
**Upstream limitations, quoted verbatim from the "Limitations and biases" section of the [model card](https://huggingface.co/ratschlab/DeepSpotM):** - Network accessline 354
**Upstream limitations, quoted verbatim from the "Limitations and biases" section of the [model card](https://huggingface.co/ratschlab/DeepSpotM):** - Network accessline 390
- [DeepSpot-M: a multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology](https://doi.org/10.64898/2026.06.19.26356060); Nonchev, Dawo, Silina, Koelzer and Rätsch; medRxiv, posted 22 June 2026. Meth - Network accessline 390
- [DeepSpot-M: a multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology](https://doi.org/10.64898/2026.06.19.26356060); Nonchev, Dawo, Silina, Koelzer and Rätsch; medRxiv, posted 22 June 2026. Meth - Network accessline 391
- [ratschlab/DeepSpotM](https://github.com/ratschlab/DeepSpotM); source code, PolyForm Noncommercial 1.0.0. - Network accessline 391
- [ratschlab/DeepSpotM](https://github.com/ratschlab/DeepSpotM); source code, PolyForm Noncommercial 1.0.0. - Network accessline 392
- [ratschlab/DeepSpotM on Hugging Face](https://huggingface.co/ratschlab/DeepSpotM); gated model weights, CC-BY-NC-SA-4.0. - Network accessline 392
- [ratschlab/DeepSpotM on Hugging Face](https://huggingface.co/ratschlab/DeepSpotM); gated model weights, CC-BY-NC-SA-4.0.
skills/deepspot-m/deepspot_m.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 71
# Quoted verbatim from the "Limitations and biases" section of the model card at # https://huggingface.co/ratschlab/DeepSpotM. They travel into every report - Network accessline 71
# Quoted verbatim from the "Limitations and biases" section of the model card at # https://huggingface.co/ratschlab/DeepSpotM. They travel into every report - Network accessline 72
# https://huggingface.co/ratschlab/DeepSpotM. They travel into every report - Network accessline 72
# https://huggingface.co/ratschlab/DeepSpotM. They travel into every report - Network accessline 440
f"{exc}. Install the model stack with " "'pip install -r skills/deepspot-m/requirements.txt', then request " f"access to https://huggingface.co/{MODEL_REPO} and run " - Network accessline 440
f"{exc}. Install the model stack with " "'pip install -r skills/deepspot-m/requirements.txt', then request " f"access to https://huggingface.co/{MODEL_REPO} and run " - Network accessline 441
"'pip install -r skills/deepspot-m/requirements.txt', then request " f"access to https://huggingface.co/{MODEL_REPO} and run " "'huggingface-cli login'. Use --demo to inspect the output format " - Network accessline 441
"'pip install -r skills/deepspot-m/requirements.txt', then request " f"access to https://huggingface.co/{MODEL_REPO} and run " "'huggingface-cli login'. Use --demo to inspect the output format " - Network accessline 442
f"access to https://huggingface.co/{MODEL_REPO} and run " - Network accessline 442
f"access to https://huggingface.co/{MODEL_REPO} and run " - Network accessline 453
f"Could not read {MODEL_REPO} at revision {MODEL_REVISION[:12]} from the " f"local Hugging Face cache ({exc}). The weights are gated: request access " f"on https://huggingface.co/{MODEL_REPO}, run 'huggingface-cli lo - Network accessline 453
f"Could not read {MODEL_REPO} at revision {MODEL_REVISION[:12]} from the " f"local Hugging Face cache ({exc}). The weights are gated: request access " f"on https://huggingface.co/{MODEL_REPO}, run 'huggingface-cli lo - Network accessline 454
f"local Hugging Face cache ({exc}). The weights are gated: request access " f"on https://huggingface.co/{MODEL_REPO}, run 'huggingface-cli login', then " "re-run with --allow-download to fetch them once. Use --demo t - Network accessline 454
f"local Hugging Face cache ({exc}). The weights are gated: request access " f"on https://huggingface.co/{MODEL_REPO}, run 'huggingface-cli login', then " "re-run with --allow-download to fetch them once. Use --demo t - Network accessline 455
f"on https://huggingface.co/{MODEL_REPO}, run 'huggingface-cli login', then " "re-run with --allow-download to fetch them once. Use --demo to inspect " "the output format without any of that." - Network accessline 455
f"on https://huggingface.co/{MODEL_REPO}, run 'huggingface-cli login', then " "re-run with --allow-download to fetch them once. Use --demo to inspect " "the output format without any of that."
skills/deepspot-m/tests/test_deepspot_m.py
skills/diff-visualizer/SKILL.md
- Network accessline 20
always: false emoji: 📈 homepage: https://github.com/ClawBio/ClawBio - Network accessline 20
always: false emoji: 📈 homepage: https://github.com/ClawBio/ClawBio - Network accessline 21
emoji: 📈 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 21
emoji: 📈 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 22
homepage: https://github.com/ClawBio/ClawBio - Network accessline 22
homepage: https://github.com/ClawBio/ClawBio - Network accessline 172
- Scanpy documentation: https://scanpy.readthedocs.io/ - Network accessline 172
- Scanpy documentation: https://scanpy.readthedocs.io/ - Network accessline 173
- Matplotlib documentation: https://matplotlib.org/ - Network accessline 173
- Matplotlib documentation: https://matplotlib.org/
skills/diff-visualizer/diff_visualizer.py
skills/diff-visualizer/tests/test_diff_visualizer.py
skills/dnasp/CONTRIBUTORS.md
- Network accessline 5
**David De Lorenzo** ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) - Network accessline 5
**David De Lorenzo** ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) - Network accessline 14
**Julio Rozas** ([@JulioRozas](https://github.com/JulioRozas)) - Network accessline 14
**Julio Rozas** ([@JulioRozas](https://github.com/JulioRozas)) - Network accessline 22
> Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, > Sánchez-Gracia A (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. > *Mol. Biol. Evol.* 34:3299-3302. https://doi.org/10.1093 - Network accessline 22
> Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, > Sánchez-Gracia A (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. > *Mol. Biol. Evol.* 34:3299-3302. https://doi.org/10.1093 - Network accessline 24
> *Mol. Biol. Evol.* 34:3299-3302. https://doi.org/10.1093/molbev/msx248 - Network accessline 24
> *Mol. Biol. Evol.* 34:3299-3302. https://doi.org/10.1093/molbev/msx248
skills/dnasp/SKILL.md
- Broad permissionsline 1
Unsupported or unresolved allowed-tools declaration - Broad permissionsline 1
Unsupported or unresolved allowed-tools declaration - Network accessline 177
always: false emoji: '' homepage: https://github.com/ClawBio/ClawBio - Network accessline 177
always: false emoji: '' homepage: https://github.com/ClawBio/ClawBio - Network accessline 178
emoji: '' homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 178
emoji: '' homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 179
homepage: https://github.com/ClawBio/ClawBio - Network accessline 179
homepage: https://github.com/ClawBio/ClawBio
skills/dnasp/dnasp.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Dangerous shell operationline 33
recombination : Minimum recombination events Rm (Hudson & Kaplan 1985) - Dangerous shell operationline 33
recombination : Minimum recombination events Rm (Hudson & Kaplan 1985) - Dangerous shell operationline 1793
"""DnaSP 6's Rm reduction (CODIGO2.vb::RecombinacionRM), applied to the - Dangerous shell operationline 1793
"""DnaSP 6's Rm reduction (CODIGO2.vb::RecombinacionRM), applied to the - Dangerous shell operationline 1839
"""Minimum recombination events Rm (Hudson & Kaplan 1985). - Dangerous shell operationline 1839
"""Minimum recombination events Rm (Hudson & Kaplan 1985). - Dangerous shell operationline 1844
and j. Rm is then DnaSP's reduction of that interval set - Dangerous shell operationline 1844
and j. Rm is then DnaSP's reduction of that interval set - Dangerous shell operationline 5775
" recombination Minimum recombination events Rm (four-gamete test)\n" - Dangerous shell operationline 5775
" recombination Minimum recombination events Rm (four-gamete test)\n"
skills/dnasp/docs/index.md
- Dangerous shell operationline 106
`recombination` uses biallelic four-gamete incompatibilities. Rm follows the - Dangerous shell operationline 106
`recombination` uses biallelic four-gamete incompatibilities. Rm follows the - Network accessline 389
- Rozas et al. (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution 34:3299-3302. https://doi.org/10.1093/molbev/msx248 - Network accessline 389
- Rozas et al. (2017). DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Molecular Biology and Evolution 34:3299-3302. https://doi.org/10.1093/molbev/msx248 - Network accessline 390
Sets. Molecular Biology and Evolution 34:3299-3302. https://doi.org/10.1093/molbev/msx248 - Rozas, Gullaud, Blandin and Aguade (2001). DNA Variation at the rp49 Gene Region - Network accessline 390
Sets. Molecular Biology and Evolution 34:3299-3302. https://doi.org/10.1093/molbev/msx248 - Rozas, Gullaud, Blandin and Aguade (2001). DNA Variation at the rp49 Gene Region - Network accessline 391
https://doi.org/10.1093/molbev/msx248 - Network accessline 391
https://doi.org/10.1093/molbev/msx248 - Network accessline 392
- Rozas, Gullaud, Blandin and Aguade (2001). DNA Variation at the rp49 Gene Region of Drosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure. Genetics 158:1147-1155. https://doi.org/10.1093/genetics/158.3.1147 - Network accessline 392
- Rozas, Gullaud, Blandin and Aguade (2001). DNA Variation at the rp49 Gene Region of Drosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure. Genetics 158:1147-1155. https://doi.org/10.1093/genetics/158.3.1147 - Network accessline 393
of Drosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure. Genetics 158:1147-1155. https://doi.org/10.1093/genetics/158.3.1147 - DnaSP 6.12 documentation: https://www.ub.edu/dnasp/DnaSP6_Documentation_6.12.pdf - Network accessline 393
of Drosophila simulans: Evolutionary Inferences From an Unusual Haplotype Structure. Genetics 158:1147-1155. https://doi.org/10.1093/genetics/158.3.1147 - DnaSP 6.12 documentation: https://www.ub.edu/dnasp/DnaSP6_Documentation_6.12.pdf - Network accessline 394
Structure. Genetics 158:1147-1155. https://doi.org/10.1093/genetics/158.3.1147 - Network accessline 394
Structure. Genetics 158:1147-1155. https://doi.org/10.1093/genetics/158.3.1147 - Network accessline 395
- DnaSP 6.12 documentation: https://www.ub.edu/dnasp/DnaSP6_Documentation_6.12.pdf - Network accessline 395
- DnaSP 6.12 documentation: https://www.ub.edu/dnasp/DnaSP6_Documentation_6.12.pdf - Network accessline 396
- Watterson (1975). On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7:256-276. https://doi.org/10.1016/0040-5809(75)90020-9 - Network accessline 396
- Watterson (1975). On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7:256-276. https://doi.org/10.1016/0040-5809(75)90020-9 - Network accessline 397
recombination. Theoretical Population Biology 7:256-276. https://doi.org/10.1016/0040-5809(75)90020-9 - Tajima (1983). Evolutionary relationship of DNA sequences in finite populations. - Network accessline 397
recombination. Theoretical Population Biology 7:256-276. https://doi.org/10.1016/0040-5809(75)90020-9 - Tajima (1983). Evolutionary relationship of DNA sequences in finite populations. - Network accessline 398
https://doi.org/10.1016/0040-5809(75)90020-9 - Network accessline 398
https://doi.org/10.1016/0040-5809(75)90020-9 - Network accessline 400
Genetics 105:437-460. https://doi.org/10.1093/genetics/105.2.437 - Network accessline 400
Genetics 105:437-460. https://doi.org/10.1093/genetics/105.2.437 - Network accessline 410
- Phipson and Smyth (2010). Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Statistical Applications in Genetics and Molecular Biology 9:Article 39. https://doi.org/10.2202/154 - Network accessline 410
- Phipson and Smyth (2010). Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn. Statistical Applications in Genetics and Molecular Biology 9:Article 39. https://doi.org/10.2202/154 - Network accessline 412
Genetics and Molecular Biology 9:Article 39. https://doi.org/10.2202/1544-6115.1585 - Network accessline 412
Genetics and Molecular Biology 9:Article 39. https://doi.org/10.2202/1544-6115.1585
skills/dnasp/environment.yml
- Executable scriptline 1
Executable file
skills/dnasp/tests/fixtures/historical_comparisons.json
skills/dnasp/tests/test_clawbio_intents.py
skills/dnasp/tests/test_coalescent_pvalues.py
skills/dnasp/tests/test_dnasp.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Dangerous shell operationline 725
# All 4 gametes present → 1 incompatible pair → Rm = 1 - Dangerous shell operationline 725
# All 4 gametes present → 1 incompatible pair → Rm = 1 - Dangerous shell operationline 734
# Sites: 1-2 incompat, 2-3 incompat, 1-3 incompat → Rm = 2 - Dangerous shell operationline 734
# Sites: 1-2 incompat, 2-3 incompat, 1-3 incompat → Rm = 2 - Dangerous shell operationline 745
# Rm = 2 (2 recombination events explain all 3 pairs) - Dangerous shell operationline 745
# Rm = 2 (2 recombination events explain all 3 pairs) - Dangerous shell operationline 769
# 7->10, DmelOSRegion Rm 5->7) when this skill used an optimal - Dangerous shell operationline 769
# 7->10, DmelOSRegion Rm 5->7) when this skill used an optimal
skills/dnasp/tests/test_historical_comparisons.py
skills/dnasp/tests/test_release_regressions.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 31
def test_nexus_quoted_labels_symbols_and_interleave(tmp_path): p = tmp_path / 'quoted.nex' p.write_text("#NEXUS\nbegin data; dimensions ntax=3 nchar=6;\nformat datatype=dna interleave=yes missing=X gap=~ matchchar=.;\nmatrix\n'a sam - Network accessline 31
def test_nexus_quoted_labels_symbols_and_interleave(tmp_path): p = tmp_path / 'quoted.nex' p.write_text("#NEXUS\nbegin data; dimensions ntax=3 nchar=6;\nformat datatype=dna interleave=yes missing=X gap=~ matchchar=.;\nmatrix\n'a sam - Network accessline 32
p = tmp_path / 'quoted.nex' p.write_text("#NEXUS\nbegin data; dimensions ntax=3 nchar=6;\nformat datatype=dna interleave=yes missing=X gap=~ matchchar=.;\nmatrix\n'a sample' AAA\nb AAT\nc AAC\n\n'a sample' AAX\nb ..~\nc ...\n; end;", en - Network accessline 32
p = tmp_path / 'quoted.nex' p.write_text("#NEXUS\nbegin data; dimensions ntax=3 nchar=6;\nformat datatype=dna interleave=yes missing=X gap=~ matchchar=.;\nmatrix\n'a sample' AAA\nb AAT\nc AAC\n\n'a sample' AAX\nb ..~\nc ...\n; end;", en - Network accessline 33
p.write_text("#NEXUS\nbegin data; dimensions ntax=3 nchar=6;\nformat datatype=dna interleave=yes missing=X gap=~ matchchar=.;\nmatrix\n'a sample' AAA\nb AAT\nc AAC\n\n'a sample' AAX\nb ..~\nc ...\n; end;", encoding='utf-8') - Network accessline 33
p.write_text("#NEXUS\nbegin data; dimensions ntax=3 nchar=6;\nformat datatype=dna interleave=yes missing=X gap=~ matchchar=.;\nmatrix\n'a sample' AAA\nb AAT\nc AAC\n\n'a sample' AAX\nb ..~\nc ...\n; end;", encoding='utf-8')
skills/dnasp/tests/test_skill_contract.py
skills/dnasp/tests/test_validation5_regressions.py
skills/dnasp/tests/test_windows_encoding.py
skills/drug-photo/SKILL.md
- Network accessline 17
always: false emoji: 📸 homepage: https://github.com/ClawBio/ClawBio - Network accessline 17
always: false emoji: 📸 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
emoji: 📸 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 18
emoji: 📸 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 151
- [CPIC Guidelines](https://cpicpgx.org/) — Clinical Pharmacogenetics Implementation Consortium - Network accessline 151
- [CPIC Guidelines](https://cpicpgx.org/) — Clinical Pharmacogenetics Implementation Consortium - Network accessline 152
- [FDA Table of Pharmacogenomic Biomarkers](https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling) — FDA-approved PGx drug labels - Network accessline 152
- [FDA Table of Pharmacogenomic Biomarkers](https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling) — FDA-approved PGx drug labels
skills/drug-repurposing-screen/SKILL.md
- Network accessline 84
always: false emoji: "💊" homepage: https://github.com/ClawBio/ClawBio - Network accessline 84
always: false emoji: "💊" homepage: https://github.com/ClawBio/ClawBio - Network accessline 85
emoji: "💊" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 85
emoji: "💊" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 86
homepage: https://github.com/ClawBio/ClawBio - Network accessline 86
homepage: https://github.com/ClawBio/ClawBio - Network accessline 365
- [Corsello et al. 2020, Nature Cancer](https://www.nature.com/articles/s43018-019-0018-6); reference dataset used to validate the pipeline - Network accessline 365
- [Corsello et al. 2020, Nature Cancer](https://www.nature.com/articles/s43018-019-0018-6); reference dataset used to validate the pipeline - Network accessline 366
- [DepMap Repurposing Hub](https://depmap.org/repurposing); compound panel and metadata - Network accessline 366
- [DepMap Repurposing Hub](https://depmap.org/repurposing); compound panel and metadata - Network accessline 367
- [Broad Repurposing Hub](https://repo-hub.broadinstitute.org/repurposing); compound metadata anchor - Network accessline 367
- [Broad Repurposing Hub](https://repo-hub.broadinstitute.org/repurposing); compound metadata anchor
skills/drug-repurposing-screen/drug_repurposing_screen.py
skills/drug-repurposing-screen/generate_demo_bundle.py
skills/drug-repurposing-screen/screen_engine.py
skills/drug-repurposing-screen/tests/__init__.py
skills/drug-repurposing-screen/tests/test_drug_repurposing_screen.py
skills/drug-repurposing-screen/tests/test_generate_demo_bundle.py
skills/ena-fetch/SKILL.md
- Network accessline 80
always: false emoji: "🧬" homepage: https://www.ebi.ac.uk/ena/browser/ - Network accessline 80
always: false emoji: "🧬" homepage: https://www.ebi.ac.uk/ena/browser/ - Network accessline 81
emoji: "🧬" homepage: https://www.ebi.ac.uk/ena/browser/ os: - Network accessline 81
emoji: "🧬" homepage: https://www.ebi.ac.uk/ena/browser/ os: - Network accessline 82
homepage: https://www.ebi.ac.uk/ena/browser/ - Network accessline 82
homepage: https://www.ebi.ac.uk/ena/browser/ - Network accessline 201
# Download script from that samplesheet (writes a script; runs nothing) python skills/ena-fetch/ena_fetch.py \ --command download-script --accession PRJEB56029 --tool curl --output /tmp/ena - Network accessline 201
# Download script from that samplesheet (writes a script; runs nothing) python skills/ena-fetch/ena_fetch.py \ --command download-script --accession PRJEB56029 --tool curl --output /tmp/ena - Network accessline 202
python skills/ena-fetch/ena_fetch.py --command download-script --accession PRJEB56029 --tool curl --output /tmp/ena - Network accessline 202
python skills/ena-fetch/ena_fetch.py --command download-script --accession PRJEB56029 --tool curl --output /tmp/ena - Network accessline 203
--command download-script --accession PRJEB56029 --tool curl --output /tmp/ena - Network accessline 203
--command download-script --accession PRJEB56029 --tool curl --output /tmp/ena - Network accessline 264
sample,fastq_1,fastq_2,strandedness SAMEA111350648,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_2.fastq.gz,auto - Network accessline 264
sample,fastq_1,fastq_2,strandedness SAMEA111350648,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_2.fastq.gz,auto - Network accessline 265
SAMEA111350648,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_2.fastq.gz,auto - Network accessline 265
SAMEA111350648,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/053/ERR10181253/ERR10181253_2.fastq.gz,auto - Network accessline 266
SAMEA111350649,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/ERR10181254_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/ERR10181254_2.fastq.gz,auto - Network accessline 266
SAMEA111350649,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/ERR10181254_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/ERR10181254_2.fastq.gz,auto - Network accessline 341
protocol despite the hostname, so opening FTP ports achieves nothing. See [docs/data-handling.md](../../docs/data-handling.md#allowlisting-for-the-public-archive-skills). Confirm with `curl -sI https://ftp.sra.ebi.ac.uk/vol1/ -o /dev/nu - Network accessline 341
protocol despite the hostname, so opening FTP ports achieves nothing. See [docs/data-handling.md](../../docs/data-handling.md#allowlisting-for-the-public-archive-skills). Confirm with `curl -sI https://ftp.sra.ebi.ac.uk/vol1/ -o /dev/nu - Network accessline 342
[docs/data-handling.md](../../docs/data-handling.md#allowlisting-for-the-public-archive-skills). Confirm with `curl -sI https://ftp.sra.ebi.ac.uk/vol1/ -o /dev/null -w '%{http_code}\n'`: `200` means reachable, `000` means blocked. The s - Network accessline 342
[docs/data-handling.md](../../docs/data-handling.md#allowlisting-for-the-public-archive-skills). Confirm with `curl -sI https://ftp.sra.ebi.ac.uk/vol1/ -o /dev/null -w '%{http_code}\n'`: `200` means reachable, `000` means blocked. The s - Network accessline 343
`curl -sI https://ftp.sra.ebi.ac.uk/vol1/ -o /dev/null -w '%{http_code}\n'`: - Network accessline 343
`curl -sI https://ftp.sra.ebi.ac.uk/vol1/ -o /dev/null -w '%{http_code}\n'`: - Network accessline 419
- [ENA Portal API](https://www.ebi.ac.uk/ena/portal/api/) and - Network accessline 419
- [ENA Portal API](https://www.ebi.ac.uk/ena/portal/api/) and - Network accessline 420
[ENA Browser API](https://www.ebi.ac.uk/ena/browser/api/); the endpoints used. - Network accessline 420
[ENA Browser API](https://www.ebi.ac.uk/ena/browser/api/); the endpoints used. - Network accessline 421
- [nf-core/rnaseq](https://nf-co.re/rnaseq) and - Network accessline 421
- [nf-core/rnaseq](https://nf-co.re/rnaseq) and - Network accessline 422
[nf-core/scrnaseq](https://nf-co.re/scrnaseq); the samplesheet contracts. - Network accessline 422
[nf-core/scrnaseq](https://nf-co.re/scrnaseq); the samplesheet contracts. - Network accessline 423
- Demo fixture: [PRJEB56029](https://www.ebi.ac.uk/ena/browser/view/PRJEB56029), - Network accessline 423
- Demo fixture: [PRJEB56029](https://www.ebi.ac.uk/ena/browser/view/PRJEB56029), - Network accessline 424
Arabidopsis thaliana RNA-seq; ENA records are open data. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 424
Arabidopsis thaliana RNA-seq; ENA records are open data. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 425
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`ena/`, plus `fastq-download-script/` folded in as - Network accessline 425
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`ena/`, plus `fastq-download-script/` folded in as - Network accessline 426
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`ena/`, plus `fastq-download-script/` folded in as `download-script`), © 2026 UK Dementia Research Institute, MIT. - Network accessline 426
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`ena/`, plus `fastq-download-script/` folded in as `download-script`), © 2026 UK Dementia Research Institute, MIT.
skills/ena-fetch/ena_fetch.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 78
p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " - Network accessline 78
p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " - Network accessline 79
help="download-script transfer tool; curl is the default " - Network accessline 79
help="download-script transfer tool; curl is the default " - Network accessline 322
output_dir, title=f"ENA report — {accession}", source_url=f"[European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/view/{accession})", - Network accessline 322
output_dir, title=f"ENA report — {accession}", source_url=f"[European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/view/{accession})", - Network accessline 323
title=f"ENA report — {accession}", source_url=f"[European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/view/{accession})", sections=sections, - Network accessline 323
title=f"ENA report — {accession}", source_url=f"[European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/view/{accession})", sections=sections, - Network accessline 324
source_url=f"[European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/view/{accession})", - Network accessline 324
source_url=f"[European Nucleotide Archive](https://www.ebi.ac.uk/ena/browser/view/{accession})",
skills/ena-fetch/ena_fetch_api.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Uses the ENA Portal API (https://www.ebi.ac.uk/ena/portal/api/) for metadata / - Network accessline 8
Uses the ENA Portal API (https://www.ebi.ac.uk/ena/portal/api/) for metadata / - Network accessline 33
PORTAL = "https://www.ebi.ac.uk/ena/portal/api" - Network accessline 33
PORTAL = "https://www.ebi.ac.uk/ena/portal/api" - Network accessline 34
BROWSER = "https://www.ebi.ac.uk/ena/browser/api" - Network accessline 34
BROWSER = "https://www.ebi.ac.uk/ena/browser/api" - Network accessline 47
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 47
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 48
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 48
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 49
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 49
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 50
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 50
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 131
`ftp://` is rewritten (these skills never speak FTP), `http(s)://` passes through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 131
`ftp://` is rewritten (these skills never speak FTP), `http(s)://` passes through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 132
through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 132
through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 590
return dest print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 590
return dest print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 591
print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 591
print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 592
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 592
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 593
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 593
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh:
skills/ena-fetch/tests/test_ena_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 27
TO_HTTPS_CASES = [ ("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 27
TO_HTTPS_CASES = [ ("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 28
("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 28
("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 29
("https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 29
("https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 30
("http://example.org/x.fastq.gz", "http://example.org/x.fastq.gz"), - Network accessline 30
("http://example.org/x.fastq.gz", "http://example.org/x.fastq.gz"), - Network accessline 32
("ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 32
("ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 191
rows = list(csv.DictReader((tmp_path / "fastq_md5.tsv").open(), delimiter="\t")) md5 = {r["url"]: r["md5"] for r in rows} assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" - Network accessline 191
rows = list(csv.DictReader((tmp_path / "fastq_md5.tsv").open(), delimiter="\t")) md5 = {r["url"]: r["md5"] for r in rows} assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" - Network accessline 192
md5 = {r["url"]: r["md5"] for r in rows} assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" "ERR10181254_1.fastq.gz"] == "735252236e07db9324a1a95112b237e9" - Network accessline 192
md5 = {r["url"]: r["md5"] for r in rows} assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" "ERR10181254_1.fastq.gz"] == "735252236e07db9324a1a95112b237e9" - Network accessline 193
assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" - Network accessline 193
assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" - Network accessline 194
"ERR10181254_1.fastq.gz"] == "735252236e07db9324a1a95112b237e9" assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" "ERR10181254_2.fastq.gz"] == "b3c6d69a99c420b3385970bf82af1fde" - Network accessline 194
"ERR10181254_1.fastq.gz"] == "735252236e07db9324a1a95112b237e9" assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" "ERR10181254_2.fastq.gz"] == "b3c6d69a99c420b3385970bf82af1fde" - Network accessline 195
assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" - Network accessline 195
assert md5["https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/054/ERR10181254/" - Network accessline 205
body = (tmp_path / "download_ena.sh").read_text() checks = [ln for ln in body.splitlines() if ln.startswith("verify_md5 ")] downloads = [ln for ln in body.splitlines() if ln.startswith("curl -fsSL")] - Network accessline 205
body = (tmp_path / "download_ena.sh").read_text() checks = [ln for ln in body.splitlines() if ln.startswith("verify_md5 ")] downloads = [ln for ln in body.splitlines() if ln.startswith("curl -fsSL")] - Network accessline 206
checks = [ln for ln in body.splitlines() if ln.startswith("verify_md5 ")] downloads = [ln for ln in body.splitlines() if ln.startswith("curl -fsSL")] assert len(checks) == len(downloads) > 0 - Network accessline 206
checks = [ln for ln in body.splitlines() if ln.startswith("verify_md5 ")] downloads = [ln for ln in body.splitlines() if ln.startswith("curl -fsSL")] assert len(checks) == len(downloads) > 0 - Network accessline 207
downloads = [ln for ln in body.splitlines() if ln.startswith("curl -fsSL")] - Network accessline 207
downloads = [ln for ln in body.splitlines() if ln.startswith("curl -fsSL")]
skills/eqtl-catalogue-region-fetch/SKILL.md
- Network accessline 57
- examples/input.json endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # tabix-on-FTP (the only network source) - Network accessline 57
- examples/input.json endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # tabix-on-FTP (the only network source) - Network accessline 58
endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # tabix-on-FTP (the only network source) data: - Network accessline 58
endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # tabix-on-FTP (the only network source) data: - Network accessline 59
- https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # tabix-on-FTP (the only network source) - Network accessline 59
- https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # tabix-on-FTP (the only network source) - Network accessline 69
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 69
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 70
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 70
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 71
homepage: https://github.com/ClawBio/ClawBio - Network accessline 71
homepage: https://github.com/ClawBio/ClawBio - Network accessline 91
eQTL Catalogue (Kerimov 2021 *Nat Genet*) is the de facto umbrella aggregator for ~50 cohorts of cis-QTL summary statistics — GTEx v8/v10, GENCORD, BLUEPRINT, BrainSeq, ROSMAP, Quach 2016, Schmiedel 2018, Lepik 2017, and more. Per-dataset s - Network accessline 91
eQTL Catalogue (Kerimov 2021 *Nat Genet*) is the de facto umbrella aggregator for ~50 cohorts of cis-QTL summary statistics — GTEx v8/v10, GENCORD, BLUEPRINT, BrainSeq, ROSMAP, Quach 2016, Schmiedel 2018, Lepik 2017, and more. Per-dataset s - Network accessline 103
- A **point lookup of one variant in one tissue**: query the GTEx Portal REST API (`https://gtexportal.org/api/v2/`) directly for single-variant queries. - **All eQTLs for a gene across all tissues**: this skill returns one (study × tissue - Network accessline 103
- A **point lookup of one variant in one tissue**: query the GTEx Portal REST API (`https://gtexportal.org/api/v2/`) directly for single-variant queries. - **All eQTLs for a gene across all tissues**: this skill returns one (study × tissue - Network accessline 105
- **Protein QTLs beyond one plasma dataset**: the catalogue carries a single protein dataset, QTD000584 (Sun 2018 INTERVAL plasma SomaScan data, which the catalogue reprocessed and added in release 6 as its first protein QTL dataset: 3,215 - Network accessline 105
- **Protein QTLs beyond one plasma dataset**: the catalogue carries a single protein dataset, QTD000584 (Sun 2018 INTERVAL plasma SomaScan data, which the catalogue reprocessed and added in release 6 as its first protein QTL dataset: 3,215 - Network accessline 107
- **Fine-mapping credible sets / PIPs**: credible-set posteriors (SuSiE) live at a different FTP path (`http://ftp.ebi.ac.uk/pub/databases/spot/eQTL/susie/`) and require a separate skill. For SuSiE / SuSiE-inf / ABF fine-mapping with PIPs a - Network accessline 107
- **Fine-mapping credible sets / PIPs**: credible-set posteriors (SuSiE) live at a different FTP path (`http://ftp.ebi.ac.uk/pub/databases/spot/eQTL/susie/`) and require a separate skill. For SuSiE / SuSiE-inf / ABF fine-mapping with PIPs a - Network accessline 117
1. **Resolve `dataset_id`**: the canonical `QTD######` identifier. Look it up in the table bundled with this skill (`data/dataset_index_r7.tsv`, derived from the catalogue's [`tabix_ftp_paths.tsv`](https://github.com/eQTL-Catalogue/eQTL-Cat - Network accessline 117
1. **Resolve `dataset_id`**: the canonical `QTD######` identifier. Look it up in the table bundled with this skill (`data/dataset_index_r7.tsv`, derived from the catalogue's [`tabix_ftp_paths.tsv`](https://github.com/eQTL-Catalogue/eQTL-Cat - Network accessline 243
6. **Dataset metadata comes from the bundled table, and the API is gone.** The catalogue permanently disabled its metadata REST API in September 2026 (it answers HTTP 410; [eQTL-Catalogue-resources#59](https://github.com/eQTL-Catalogue/eQTL - Network accessline 243
6. **Dataset metadata comes from the bundled table, and the API is gone.** The catalogue permanently disabled its metadata REST API in September 2026 (it answers HTTP 410; [eQTL-Catalogue-resources#59](https://github.com/eQTL-Catalogue/eQTL - Network accessline 247
8. **One row per variant, not one row per rsID.** The catalogue stores one rsID per line, so a variant with several rsIDs is written on several lines with identical statistics, and its [FAQ](https://www.ebi.ac.uk/eqtl/Data_access/) recommen - Network accessline 247
8. **One row per variant, not one row per rsID.** The catalogue stores one rsID per line, so a variant with several rsIDs is written on several lines with identical statistics, and its [FAQ](https://www.ebi.ac.uk/eqtl/Data_access/) recommen - Network accessline 268
- Kerimov et al. (2021). *A compendium of uniformly processed human gene expression and splicing quantitative trait loci.* Nat Genet 53, 1290-1299. doi:10.1038/s41588-021-00924-w - Per-dataset citation list at <https://www.ebi.ac.uk/eqtl/St - Network accessline 268
- Kerimov et al. (2021). *A compendium of uniformly processed human gene expression and splicing quantitative trait loci.* Nat Genet 53, 1290-1299. doi:10.1038/s41588-021-00924-w - Per-dataset citation list at <https://www.ebi.ac.uk/eqtl/St - Network accessline 269
- Per-dataset citation list at <https://www.ebi.ac.uk/eqtl/Studies/>. - Network accessline 269
- Per-dataset citation list at <https://www.ebi.ac.uk/eqtl/Studies/>.
skills/eqtl-catalogue-region-fetch/data/dataset_index_r7.provenance.json
- Network accessline 20
"derived_on": "2026-09-12", "source_file": "tabix/tabix_ftp_paths.tsv", "source_url": "https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv", - Network accessline 20
"derived_on": "2026-09-12", "source_file": "tabix/tabix_ftp_paths.tsv", "source_url": "https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv", - Network accessline 21
"source_file": "tabix/tabix_ftp_paths.tsv", "source_url": "https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv", "source_repository": "https://github.com/eQTL-Catalogue/eQTL-Catalog - Network accessline 21
"source_file": "tabix/tabix_ftp_paths.tsv", "source_url": "https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv", "source_repository": "https://github.com/eQTL-Catalogue/eQTL-Catalog - Network accessline 22
"source_url": "https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv", - Network accessline 22
"source_url": "https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv", - Network accessline 23
"source_repository": "https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources", - Network accessline 23
"source_repository": "https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources", - Network accessline 38
}, "why_derived": "ClawBio's wheel build hook (hatch_build.py, SMALL_DATA_MAX_BYTES = 262144) drops non-headline skill data files over 256 KB; the source table is 287,387 bytes.", "why_bundled": "The catalogue's metadata REST API was pe - Network accessline 38
}, "why_derived": "ClawBio's wheel build hook (hatch_build.py, SMALL_DATA_MAX_BYTES = 262144) drops non-headline skill data files over 256 KB; the source table is 287,387 bytes.", "why_bundled": "The catalogue's metadata REST API was pe - Network accessline 39
"why_derived": "ClawBio's wheel build hook (hatch_build.py, SMALL_DATA_MAX_BYTES = 262144) drops non-headline skill data files over 256 KB; the source table is 287,387 bytes.", "why_bundled": "The catalogue's metadata REST API was permane - Network accessline 39
"why_derived": "ClawBio's wheel build hook (hatch_build.py, SMALL_DATA_MAX_BYTES = 262144) drops non-headline skill data files over 256 KB; the source table is 287,387 bytes.", "why_bundled": "The catalogue's metadata REST API was permane - Network accessline 40
"why_bundled": "The catalogue's metadata REST API was permanently disabled in September 2026; the maintainer confirmed it on our issue, https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59 (closed 2026-09-09). This table is - Network accessline 40
"why_bundled": "The catalogue's metadata REST API was permanently disabled in September 2026; the maintainer confirmed it on our issue, https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59 (closed 2026-09-09). This table is - Network accessline 41
"licence": "CC-BY-4.0 (https://www.ebi.ac.uk/eqtl/License/)", - Network accessline 41
"licence": "CC-BY-4.0 (https://www.ebi.ac.uk/eqtl/License/)", - Network accessline 42
"licence_note": "The eQTL Catalogue licence page states, in one sentence covering both halves: \"All eQTL Catalogue code is distributed under Apache 2.0 license and all its data is distributed under Creative Commons Attribution 4.0 Internat - Network accessline 42
"licence_note": "The eQTL Catalogue licence page states, in one sentence covering both halves: \"All eQTL Catalogue code is distributed under Apache 2.0 license and all its data is distributed under Creative Commons Attribution 4.0 Internat - Network accessline 43
"attribution": "eQTL Catalogue dataset index. Source: eQTL Catalogue published tabix path table, tabix/tabix_ftp_paths.tsv, from the eQTL-Catalogue/eQTL-Catalogue-resources repository (https://github.com/eQTL-Catalogue/eQTL-Catalogue-resour - Network accessline 43
"attribution": "eQTL Catalogue dataset index. Source: eQTL Catalogue published tabix path table, tabix/tabix_ftp_paths.tsv, from the eQTL-Catalogue/eQTL-Catalogue-resources repository (https://github.com/eQTL-Catalogue/eQTL-Catalogue-resour
skills/eqtl-catalogue-region-fetch/eqtl_catalogue_region_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 8
Source: eQTL Catalogue v7+ (Kerimov 2021, Nat Genet 53:1290). License: CC-BY-4.0 (https://www.ebi.ac.uk/eqtl/License/). - Network accessline 8
Source: eQTL Catalogue v7+ (Kerimov 2021, Nat Genet 53:1290). License: CC-BY-4.0 (https://www.ebi.ac.uk/eqtl/License/). - Network accessline 9
License: CC-BY-4.0 (https://www.ebi.ac.uk/eqtl/License/). - Network accessline 9
License: CC-BY-4.0 (https://www.ebi.ac.uk/eqtl/License/). - Network accessline 14
The REST API at `https://www.ebi.ac.uk/eqtl/api/v2/datasets/{id}/associations` - Network accessline 14
The REST API at `https://www.ebi.ac.uk/eqtl/api/v2/datasets/{id}/associations` - Network accessline 15
silently truncated regional fetches to one side of the TSS (verified 2026-05), and the whole API was permanently disabled by the catalogue in September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/is - Network accessline 15
silently truncated regional fetches to one side of the TSS (verified 2026-05), and the whole API was permanently disabled by the catalogue in September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/is - Network accessline 16
the whole API was permanently disabled by the catalogue in September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59). This skill reads per-variant rows from the tabix-indexed FTP files, and d - Network accessline 16
the whole API was permanently disabled by the catalogue in September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59). This skill reads per-variant rows from the tabix-indexed FTP files, and d - Network accessline 17
answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59). This skill reads per-variant rows from the tabix-indexed FTP - Network accessline 17
answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59). This skill reads per-variant rows from the tabix-indexed FTP - Network accessline 22
URL pattern (the per-variant file class, `all` or `cc`, is read from the bundled index): https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 22
URL pattern (the per-variant file class, `all` or `cc`, is read from the bundled index): https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 23
https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 23
https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 66
DEFAULT_FTP_BASE = "https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats" - Network accessline 66
DEFAULT_FTP_BASE = "https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats" - Network accessline 69
# catalogue's own published `tabix_ftp_paths.tsv` (r7, 758 datasets). The metadata # REST API this skill used for it was permanently disabled by the catalogue in # September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL- - Network accessline 69
# catalogue's own published `tabix_ftp_paths.tsv` (r7, 758 datasets). The metadata # REST API this skill used for it was permanently disabled by the catalogue in # September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL- - Network accessline 70
# REST API this skill used for it was permanently disabled by the catalogue in # September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59); # see data/dataset_index_r7.provenance.json. - Network accessline 70
# REST API this skill used for it was permanently disabled by the catalogue in # September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59); # see data/dataset_index_r7.provenance.json. - Network accessline 71
# September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59); - Network accessline 71
# September 2026 (it answers HTTP 410; https://github.com/eQTL-Catalogue/eQTL-Catalogue-resources/issues/59); - Network accessline 99
"""Records the eQTL Catalogue release pinned per fetch (for the manifest) - Network accessline 99
"""Records the eQTL Catalogue release pinned per fetch (for the manifest) - Network accessline 236
# rsIDs is written on several lines with identical statistics. The catalogue's own # FAQ says so and recommends removing the duplicates before any downstream analysis # (https://www.ebi.ac.uk/eqtl/Data_access/, read 2026-10-22). Measured on - Network accessline 236
# rsIDs is written on several lines with identical statistics. The catalogue's own # FAQ says so and recommends removing the duplicates before any downstream analysis # (https://www.ebi.ac.uk/eqtl/Data_access/, read 2026-10-22). Measured on - Network accessline 237
# FAQ says so and recommends removing the duplicates before any downstream analysis # (https://www.ebi.ac.uk/eqtl/Data_access/, read 2026-10-22). Measured on the SORT1 # QTD000276 1 Mb window: 2,833 rows, 2,740 distinct (trait, variant) key - Network accessline 237
# FAQ says so and recommends removing the duplicates before any downstream analysis # (https://www.ebi.ac.uk/eqtl/Data_access/, read 2026-10-22). Measured on the SORT1 # QTD000276 1 Mb window: 2,833 rows, 2,740 distinct (trait, variant) key - Network accessline 238
# (https://www.ebi.ac.uk/eqtl/Data_access/, read 2026-10-22). Measured on the SORT1 - Network accessline 238
# (https://www.ebi.ac.uk/eqtl/Data_access/, read 2026-10-22). Measured on the SORT1 - Network accessline 453
URL pattern (verified 2026-05-05 + 2026-05-15): https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 453
URL pattern (verified 2026-05-05 + 2026-05-15): https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 454
https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 454
https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/<QTS>/<QTD>/<QTD>.<file_class>.tsv.gz - Network accessline 610
try: try: rows = tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp) - Network accessline 610
try: try: rows = tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp) - Network accessline 611
try: rows = tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp) except ValueError: - Network accessline 611
try: rows = tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp) except ValueError: - Network accessline 612
rows = tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp) - Network accessline 612
rows = tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp) - Network accessline 613
except ValueError: rows = tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp) for line in rows: - Network accessline 613
except ValueError: rows = tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp) for line in rows: - Network accessline 614
rows = tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp) - Network accessline 614
rows = tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp)
skills/eqtl-catalogue-region-fetch/examples/run_example.sh
skills/eqtl-catalogue-region-fetch/tests/conftest.py
skills/eqtl-catalogue-region-fetch/tests/test_eqtl_catalogue_region_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 42
url = ftp_url_for("QTS000015", "QTD000266") assert url == ( "https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/" - Network accessline 42
url = ftp_url_for("QTS000015", "QTD000266") assert url == ( "https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/" - Network accessline 43
assert url == ( "https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/" "QTS000015/QTD000266/QTD000266.all.tsv.gz" - Network accessline 43
assert url == ( "https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/" "QTS000015/QTD000266/QTD000266.all.tsv.gz" - Network accessline 44
"https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/" - Network accessline 44
"https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/" - Network accessline 49
def test_ftp_url_for_strips_trailing_slash_on_base(): url = ftp_url_for("QTS000015", "QTD000266", ftp_base="https://example.org/sumstats/") - Network accessline 49
def test_ftp_url_for_strips_trailing_slash_on_base(): url = ftp_url_for("QTS000015", "QTD000266", ftp_base="https://example.org/sumstats/") - Network accessline 50
url = ftp_url_for("QTS000015", "QTD000266", ftp_base="https://example.org/sumstats/") assert url == "https://example.org/sumstats/QTS000015/QTD000266/QTD000266.all.tsv.gz" - Network accessline 50
url = ftp_url_for("QTS000015", "QTD000266", ftp_base="https://example.org/sumstats/") assert url == "https://example.org/sumstats/QTS000015/QTD000266/QTD000266.all.tsv.gz" - Network accessline 51
ftp_base="https://example.org/sumstats/") - Network accessline 51
ftp_base="https://example.org/sumstats/") - Network accessline 52
assert url == "https://example.org/sumstats/QTS000015/QTD000266/QTD000266.all.tsv.gz" - Network accessline 52
assert url == "https://example.org/sumstats/QTS000015/QTD000266/QTD000266.all.tsv.gz" - Network accessline 159
def fetch(chrom, *args, **kwargs): - Network accessline 159
def fetch(chrom, *args, **kwargs):
skills/eqtl-catalogue-region-fetch/tests/test_live_eqtl_catalogue_region_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 53
def status(url: str) -> int: req = urllib.request.Request(url, method="HEAD") - Network accessline 53
def status(url: str) -> int: req = urllib.request.Request(url, method="HEAD") - Network accessline 54
req = urllib.request.Request(url, method="HEAD") - Network accessline 54
req = urllib.request.Request(url, method="HEAD") - Network accessline 55
try: with urllib.request.urlopen(req, timeout=60) as r: return r.status - Network accessline 55
try: with urllib.request.urlopen(req, timeout=60) as r: return r.status - Network accessline 56
with urllib.request.urlopen(req, timeout=60) as r: - Network accessline 56
with urllib.request.urlopen(req, timeout=60) as r:
skills/equity-scorer/SKILL.md
- Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio
skills/equity-scorer/api.py
skills/equity-scorer/equity_scorer.py
skills/equity-scorer/tests/test_equity_scorer.py
skills/equity-scorer/tests/test_repro_bundle.py
skills/fastreer/SKILL.md
- Network accessline 76
always: false emoji: "🌳" homepage: https://github.com/ClawBio/ClawBio - Network accessline 76
always: false emoji: "🌳" homepage: https://github.com/ClawBio/ClawBio - Network accessline 77
emoji: "🌳" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 77
emoji: "🌳" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 78
homepage: https://github.com/ClawBio/ClawBio - Network accessline 78
homepage: https://github.com/ClawBio/ClawBio - Network accessline 106
You are **fastreeR**, a specialised ClawBio skill for computing phylogenetic distance matrices and trees from genomic VCF or FASTA data using the [fastreeR](https://github.com/gkanogiannis/fastreeR) hybrid Java/Python toolkit. - Network accessline 106
You are **fastreeR**, a specialised ClawBio skill for computing phylogenetic distance matrices and trees from genomic VCF or FASTA data using the [fastreeR](https://github.com/gkanogiannis/fastreeR) hybrid Java/Python toolkit. - Network accessline 108
[fastreeR](https://github.com/gkanogiannis/fastreeR) hybrid Java/Python toolkit. - Network accessline 108
[fastreeR](https://github.com/gkanogiannis/fastreeR) hybrid Java/Python toolkit. - Dangerous shell operationline 309
`sudo apt install default-jre` (Linux) or `brew install openjdk@17` (macOS) - Dangerous shell operationline 309
`sudo apt install default-jre` (Linux) or `brew install openjdk@17` (macOS) - Network accessline 374
- [fastreeR GitHub](https://github.com/gkanogiannis/fastreeR): source code, documentation, and Docker image - Network accessline 374
- [fastreeR GitHub](https://github.com/gkanogiannis/fastreeR): source code, documentation, and Docker image - Network accessline 375
- [fastreeR PyPI](https://pypi.org/project/fastreer/): Python package - Network accessline 375
- [fastreeR PyPI](https://pypi.org/project/fastreer/): Python package - Network accessline 376
- [fastreeR Bioconductor](https://bioconductor.org/packages/fastreeR/): R/Bioconductor package - Network accessline 376
- [fastreeR Bioconductor](https://bioconductor.org/packages/fastreeR/): R/Bioconductor package - Network accessline 377
- Gkanogiannis A (2016) A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. *BMC Bioinformatics* 17, 311. https://doi.org/10.1186/s12859-016-1186-3 - Network accessline 377
- Gkanogiannis A (2016) A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. *BMC Bioinformatics* 17, 311. https://doi.org/10.1186/s12859-016-1186-3
skills/fastreer/fastreer.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 5
Wraps the fastreeR hybrid Java/Python toolkit (https://github.com/gkanogiannis/fastreeR). - Network accessline 5
Wraps the fastreeR hybrid Java/Python toolkit (https://github.com/gkanogiannis/fastreeR). - Dangerous shell operationline 216
" sudo apt install default-jre # Java (Debian/Ubuntu)\n" - Dangerous shell operationline 216
" sudo apt install default-jre # Java (Debian/Ubuntu)\n" - Dangerous shell operationline 431
sudo apt install default-jre # Debian/Ubuntu - Dangerous shell operationline 431
sudo apt install default-jre # Debian/Ubuntu - Network accessline 437
Gkanogiannis A (2016) A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. *BMC Bioinformatics* 17, 311. https://doi.org/10.1186/s12859-016-1186-3 - Network accessline 437
Gkanogiannis A (2016) A scalable assembly-free variable selection algorithm for biomarker discovery from metagenomes. *BMC Bioinformatics* 17, 311. https://doi.org/10.1186/s12859-016-1186-3 - Network accessline 439
https://doi.org/10.1186/s12859-016-1186-3 - Network accessline 439
https://doi.org/10.1186/s12859-016-1186-3
skills/fastreer/tests/test_fastreer.py
skills/fine-mapping/SKILL.md
- Network accessline 22
always: false emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio - Network accessline 22
always: false emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 23
emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
homepage: https://github.com/ClawBio/ClawBio - Network accessline 24
homepage: https://github.com/ClawBio/ClawBio - Network accessline 67
- **Without it**: Researchers must manually triage 10–200 correlated SNPs per locus with no principled prioritisation - **With it**: A ranked credible set with PIPs and 95% credible set boundaries in seconds - **Why ClawBio**: Runs locally - Network accessline 67
- **Without it**: Researchers must manually triage 10–200 correlated SNPs per locus with no principled prioritisation - **With it**: A ranked credible set with PIPs and 95% credible set boundaries in seconds - **Why ClawBio**: Runs locally - Network accessline 69
- **Why ClawBio**: Runs locally without uploading individual-level data; implements ABF natively and delegates SuSiE to the published [sushie](https://github.com/mancusolab/sushie) package — no R dependency required - Network accessline 69
- **Why ClawBio**: Runs locally without uploading individual-level data; implements ABF natively and delegates SuSiE to the published [sushie](https://github.com/mancusolab/sushie) package — no R dependency required - Network accessline 269
- [Wang et al. (2020) JRSS-B](https://doi.org/10.1111/rssb.12388) — SuSiE algorithm - Network accessline 269
- [Wang et al. (2020) JRSS-B](https://doi.org/10.1111/rssb.12388) — SuSiE algorithm - Network accessline 270
- [Wakefield (2009) Am J Hum Genet](https://doi.org/10.1016/j.ajhg.2008.12.010) — Approximate Bayes Factors for GWAS - Network accessline 270
- [Wakefield (2009) Am J Hum Genet](https://doi.org/10.1016/j.ajhg.2008.12.010) — Approximate Bayes Factors for GWAS - Network accessline 271
- [Cui et al. (2024) Nature Genetics](https://doi.org/10.1038/s41588-023-01597-3) — SuSiE-inf: improving fine-mapping by modeling infinitesimal effects - Network accessline 271
- [Cui et al. (2024) Nature Genetics](https://doi.org/10.1038/s41588-023-01597-3) — SuSiE-inf: improving fine-mapping by modeling infinitesimal effects
skills/fine-mapping/core/__init__.py
skills/fine-mapping/core/abf.py
skills/fine-mapping/core/credible_sets.py
skills/fine-mapping/core/io.py
skills/fine-mapping/core/report.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 301
chrom_clean = str(chrom).lstrip("chr") url = ( f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 301
chrom_clean = str(chrom).lstrip("chr") url = ( f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 302
url = ( f"https://rest.ensembl.org/overlap/region/human/" f"{chrom_clean}:{start}-{end}" - Network accessline 302
url = ( f"https://rest.ensembl.org/overlap/region/human/" f"{chrom_clean}:{start}-{end}" - Network accessline 303
f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 303
f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 305
f"?feature=gene;content-type=application/json" ) req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 305
f"?feature=gene;content-type=application/json" ) req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 307
req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 307
req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 309
for attempt in range(3): try: with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 309
for attempt in range(3): try: with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 310
try: with urllib.request.urlopen(req, timeout=10) as resp: genes = _json.loads(resp.read()) - Network accessline 310
try: with urllib.request.urlopen(req, timeout=10) as resp: genes = _json.loads(resp.read()) - Network accessline 311
with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 311
with urllib.request.urlopen(req, timeout=10) as resp:
skills/fine-mapping/core/susie.py
skills/fine-mapping/core/susie_inf.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Implements the SuSiE-inf algorithm from: Cui et al. (2024) "Improving fine-mapping by modeling infinitesimal effects" Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3 - Network accessline 4
Implements the SuSiE-inf algorithm from: Cui et al. (2024) "Improving fine-mapping by modeling infinitesimal effects" Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3 - Network accessline 6
Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3 - Network accessline 6
Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3
skills/fine-mapping/fine_mapping.py
skills/fine-mapping/fine_mapping_core/__init__.py
skills/fine-mapping/fine_mapping_core/abf.py
skills/fine-mapping/fine_mapping_core/credible_sets.py
skills/fine-mapping/fine_mapping_core/io.py
skills/fine-mapping/fine_mapping_core/report.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 301
chrom_clean = str(chrom).lstrip("chr") url = ( f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 301
chrom_clean = str(chrom).lstrip("chr") url = ( f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 302
url = ( f"https://rest.ensembl.org/overlap/region/human/" f"{chrom_clean}:{start}-{end}" - Network accessline 302
url = ( f"https://rest.ensembl.org/overlap/region/human/" f"{chrom_clean}:{start}-{end}" - Network accessline 303
f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 303
f"https://rest.ensembl.org/overlap/region/human/" - Network accessline 305
f"?feature=gene;content-type=application/json" ) req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 305
f"?feature=gene;content-type=application/json" ) req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 307
req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 307
req = urllib.request.Request(url, headers={"User-Agent": "ClawBio/1.0"}) - Network accessline 309
for attempt in range(3): try: with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 309
for attempt in range(3): try: with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 310
try: with urllib.request.urlopen(req, timeout=10) as resp: genes = _json.loads(resp.read()) - Network accessline 310
try: with urllib.request.urlopen(req, timeout=10) as resp: genes = _json.loads(resp.read()) - Network accessline 311
with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 311
with urllib.request.urlopen(req, timeout=10) as resp:
skills/fine-mapping/fine_mapping_core/susie.py
skills/fine-mapping/fine_mapping_core/susie_inf.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Implements the SuSiE-inf algorithm from: Cui et al. (2024) "Improving fine-mapping by modeling infinitesimal effects" Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3 - Network accessline 4
Implements the SuSiE-inf algorithm from: Cui et al. (2024) "Improving fine-mapping by modeling infinitesimal effects" Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3 - Network accessline 6
Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3 - Network accessline 6
Nature Genetics 56, 162–169. https://doi.org/10.1038/s41588-023-01597-3
skills/fine-mapping/tests/test_fine_mapping.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 1173
with patch("urllib.request.urlopen", side_effect=OSError("network error")): - Network accessline 1173
with patch("urllib.request.urlopen", side_effect=OSError("network error")): - Network accessline 1200
with patch("urllib.request.urlopen", side_effect=side_effects), \ - Network accessline 1200
with patch("urllib.request.urlopen", side_effect=side_effects), \ - Network accessline 1219
with patch("urllib.request.urlopen", side_effect=[http_429, http_429, http_429]), \ - Network accessline 1219
with patch("urllib.request.urlopen", side_effect=[http_429, http_429, http_429]), \ - Network accessline 1235
with patch("urllib.request.urlopen", side_effect=http_500) as mock_urlopen, \ - Network accessline 1235
with patch("urllib.request.urlopen", side_effect=http_500) as mock_urlopen, \ - Network accessline 1260
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1260
with patch("urllib.request.urlopen", return_value=mock_resp): - Network accessline 1283
with patch("urllib.request.urlopen", side_effect=capture_urlopen): - Network accessline 1283
with patch("urllib.request.urlopen", side_effect=capture_urlopen):
skills/flow-bio/SKILL.md
- Network accessline 63
always: false emoji: 🌊 homepage: https://flow.bio - Network accessline 63
always: false emoji: 🌊 homepage: https://flow.bio - Network accessline 64
emoji: 🌊 homepage: https://flow.bio os: - Network accessline 64
emoji: 🌊 homepage: https://flow.bio os: - Network accessline 65
homepage: https://flow.bio - Network accessline 65
homepage: https://flow.bio - Network accessline 202
**Key parameters**: - Base URL: `https://app.flow.bio/api` (configurable via `FLOW_URL`) - Network accessline 202
**Key parameters**: - Base URL: `https://app.flow.bio/api` (configurable via `FLOW_URL`) - Network accessline 203
- Base URL: `https://app.flow.bio/api` (configurable via `FLOW_URL`) - Network accessline 203
- Base URL: `https://app.flow.bio/api` (configurable via `FLOW_URL`) - Network accessline 255
- [Flow.bio](https://flow.bio) — Bioinformatics platform - Network accessline 255
- [Flow.bio](https://flow.bio) — Bioinformatics platform - Network accessline 256
- [Nextflow](https://nextflow.io/) — Workflow engine powering Flow pipelines - Network accessline 256
- [Nextflow](https://nextflow.io/) — Workflow engine powering Flow pipelines
skills/flow-bio/data/demo_cache.json
- Network accessline 1
{ "instance": "https://app.flow.bio/api", - Network accessline 1
{ "instance": "https://app.flow.bio/api", - Network accessline 2
"instance": "https://app.flow.bio/api", - Network accessline 2
"instance": "https://app.flow.bio/api", - Network accessline 260
"name": "GRCm39", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/", - Network accessline 260
"name": "GRCm39", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/", - Network accessline 261
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/", "created": 1592953200, - Network accessline 261
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/", "created": 1592953200, - Network accessline 262
"url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/", - Network accessline 262
"url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/", - Network accessline 328
"name": "mRatBN7.2", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/", - Network accessline 328
"name": "mRatBN7.2", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/", - Network accessline 329
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/", "created": 1604966400, - Network accessline 329
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/", "created": 1604966400, - Network accessline 330
"url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/", - Network accessline 330
"url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_015227675.2/", - Network accessline 396
"name": "GRCz11", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/", - Network accessline 396
"name": "GRCz11", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/", - Network accessline 397
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/", "created": 1494284400, - Network accessline 397
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/", "created": 1494284400, - Network accessline 398
"url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/", - Network accessline 398
"url": "https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/", - Network accessline 464
"name": "BDGP6.32", "long_name": "", "url": "https://www.ensembl.org/Drosophila_melanogaster/Info/Index", - Network accessline 464
"name": "BDGP6.32", "long_name": "", "url": "https://www.ensembl.org/Drosophila_melanogaster/Info/Index", - Network accessline 465
"long_name": "", "url": "https://www.ensembl.org/Drosophila_melanogaster/Info/Index", "created": 1596236400, - Network accessline 465
"long_name": "", "url": "https://www.ensembl.org/Drosophila_melanogaster/Info/Index", "created": 1596236400, - Network accessline 466
"url": "https://www.ensembl.org/Drosophila_melanogaster/Info/Index", - Network accessline 466
"url": "https://www.ensembl.org/Drosophila_melanogaster/Info/Index", - Network accessline 532
"name": "R64-1-1", "long_name": "", "url": "https://ncbi.nlm.nih.gov/assembly/GCF_000146045.2/", - Network accessline 532
"name": "R64-1-1", "long_name": "", "url": "https://ncbi.nlm.nih.gov/assembly/GCF_000146045.2/", - Network accessline 533
"long_name": "", "url": "https://ncbi.nlm.nih.gov/assembly/GCF_000146045.2/", "created": 1538348400, - Network accessline 533
"long_name": "", "url": "https://ncbi.nlm.nih.gov/assembly/GCF_000146045.2/", "created": 1538348400, - Network accessline 534
"url": "https://ncbi.nlm.nih.gov/assembly/GCF_000146045.2/", - Network accessline 534
"url": "https://ncbi.nlm.nih.gov/assembly/GCF_000146045.2/", - Network accessline 600
"name": "GCF_000005845.2", "long_name": "K12 substr.MG1655 GCA_000005845.ASM584v2.57", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/", - Network accessline 600
"name": "GCF_000005845.2", "long_name": "K12 substr.MG1655 GCA_000005845.ASM584v2.57", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/", - Network accessline 601
"long_name": "K12 substr.MG1655 GCA_000005845.ASM584v2.57", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/", "created": 1380240000, - Network accessline 601
"long_name": "K12 substr.MG1655 GCA_000005845.ASM584v2.57", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/", "created": 1380240000, - Network accessline 602
"url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/", - Network accessline 602
"url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000005845.2/", - Network accessline 668
"name": "GRCg7b.110", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016699485.2/", - Network accessline 668
"name": "GRCg7b.110", "long_name": "", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016699485.2/", - Network accessline 669
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016699485.2/", "created": 1611014400, - Network accessline 669
"long_name": "", "url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016699485.2/", "created": 1611014400, - Network accessline 670
"url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016699485.2/", - Network accessline 670
"url": "https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_016699485.2/", - Network accessline 736
"name": "TAIR10", "long_name": "TAIR10 Ensembl 59", "url": "https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index", - Network accessline 736
"name": "TAIR10", "long_name": "TAIR10 Ensembl 59", "url": "https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index", - Network accessline 737
"long_name": "TAIR10 Ensembl 59", "url": "https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index", "created": 1465516800, - Network accessline 737
"long_name": "TAIR10 Ensembl 59", "url": "https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index", "created": 1465516800, - Network accessline 738
"url": "https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index", - Network accessline 738
"url": "https://plants.ensembl.org/Arabidopsis_thaliana/Info/Index",
skills/flow-bio/flow_bio.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 49
DEFAULT_BASE_URL = "https://app.flow.bio/api" - Network accessline 49
DEFAULT_BASE_URL = "https://app.flow.bio/api" - Access to secretsline 75
[Credential-related source omitted] - Access to secretsline 75
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 388
[Credential-related source omitted] - Access to secretsline 388
[Credential-related source omitted] - Access to secretsline 392
[Credential-related source omitted] - Access to secretsline 392
[Credential-related source omitted] - Access to secretsline 393
[Credential-related source omitted] - Access to secretsline 393
[Credential-related source omitted] - Network accessline 990
auth_group.add_argument("--password", metavar="PASS", help="Flow password (or set FLOW_PASSWORD)") auth_group.add_argument("--token", metavar="TOKEN", help="Existing JWT token (or set FLOW_TOKEN)") auth_group.add_argument("--url", m - Network accessline 990
auth_group.add_argument("--password", metavar="PASS", help="Flow password (or set FLOW_PASSWORD)") auth_group.add_argument("--token", metavar="TOKEN", help="Existing JWT token (or set FLOW_TOKEN)") auth_group.add_argument("--url", m - Network accessline 992
auth_group.add_argument("--url", metavar="URL", help="Flow API base URL (default: https://app.flow.bio/api)") - Network accessline 992
auth_group.add_argument("--url", metavar="URL", help="Flow API base URL (default: https://app.flow.bio/api)") - Access to secretsline 1068
[Credential-related source omitted] - Access to secretsline 1068
[Credential-related source omitted] - Access to secretsline 1069
[Credential-related source omitted] - Access to secretsline 1069
[Credential-related source omitted] - Access to secretsline 1073
[Credential-related source omitted] - Access to secretsline 1073
[Credential-related source omitted] - Access to secretsline 1074
[Credential-related source omitted] - Access to secretsline 1074
[Credential-related source omitted] - Access to secretsline 1075
[Credential-related source omitted] - Access to secretsline 1075
[Credential-related source omitted]
skills/flow-bio/tests/__init__.py
skills/flow-bio/tests/test_flow_bio.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 186
import requests client._requests = requests client.base_url = "https://app.flow.bio/api" - Network accessline 186
import requests client._requests = requests client.base_url = "https://app.flow.bio/api" - Network accessline 187
[Credential-related source omitted] - Network accessline 187
[Credential-related source omitted] - Network accessline 188
client.base_url = "https://app.flow.bio/api" - Network accessline 188
client.base_url = "https://app.flow.bio/api" - Network accessline 325
def test_write_reproducibility(self, tmp_path): flow_bio.write_reproducibility(tmp_path, ["--pipelines"], "https://app.flow.bio/api") - Network accessline 325
def test_write_reproducibility(self, tmp_path): flow_bio.write_reproducibility(tmp_path, ["--pipelines"], "https://app.flow.bio/api") - Network accessline 326
flow_bio.write_reproducibility(tmp_path, ["--pipelines"], "https://app.flow.bio/api") - Network accessline 326
flow_bio.write_reproducibility(tmp_path, ["--pipelines"], "https://app.flow.bio/api") - Network accessline 330
assert "skills/flow-bio/flow_bio.py" in content assert "--pipelines" in content assert "https://app.flow.bio/api" in content - Network accessline 330
assert "skills/flow-bio/flow_bio.py" in content assert "--pipelines" in content assert "https://app.flow.bio/api" in content - Network accessline 332
assert "https://app.flow.bio/api" in content - Network accessline 332
assert "https://app.flow.bio/api" in content
skills/galaxy-bridge/SKILL.md
- Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 24
[Credential-related source omitted] - Network accessline 25
always: false emoji: 🌌 homepage: https://github.com/ClawBio/ClawBio - Network accessline 25
always: false emoji: 🌌 homepage: https://github.com/ClawBio/ClawBio - Network accessline 26
emoji: 🌌 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 26
emoji: 🌌 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 27
homepage: https://github.com/ClawBio/ClawBio - Network accessline 27
homepage: https://github.com/ClawBio/ClawBio - Access to secretsline 113
[Credential-related source omitted] - Access to secretsline 113
[Credential-related source omitted] - Network accessline 197
**Optional (for execution):** - `GALAXY_URL` environment variable (default: `https://usegalaxy.org`) - Network accessline 197
**Optional (for execution):** - `GALAXY_URL` environment variable (default: `https://usegalaxy.org`) - Network accessline 198
- `GALAXY_URL` environment variable (default: `https://usegalaxy.org`) - Network accessline 198
- `GALAXY_URL` environment variable (default: `https://usegalaxy.org`) - Access to secretsline 199
[Credential-related source omitted] - Access to secretsline 199
[Credential-related source omitted] - Network accessline 221
- [Galaxy Project](https://galaxyproject.org/) — Afgan et al. (2018) Nucleic Acids Research - Network accessline 221
- [Galaxy Project](https://galaxyproject.org/) — Afgan et al. (2018) Nucleic Acids Research - Network accessline 222
- [BioBlend](https://bioblend.readthedocs.io/) — Sloggett et al. (2013) Bioinformatics - Network accessline 222
- [BioBlend](https://bioblend.readthedocs.io/) — Sloggett et al. (2013) Bioinformatics - Network accessline 223
- [usegalaxy.org](https://usegalaxy.org/) — Main Galaxy public server - Network accessline 223
- [usegalaxy.org](https://usegalaxy.org/) — Main Galaxy public server - Network accessline 224
- [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/) — Community tool repository - Network accessline 224
- [Galaxy ToolShed](https://toolshed.g2.bx.psu.edu/) — Community tool repository
skills/galaxy-bridge/demo/reproducibility/commands.sh
skills/galaxy-bridge/galaxy_bridge.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 46
DEFAULT_GALAXY_URL = "https://usegalaxy.org" - Network accessline 46
DEFAULT_GALAXY_URL = "https://usegalaxy.org" - Access to secretsline 130
[Credential-related source omitted] - Access to secretsline 130
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Access to secretsline 133
[Credential-related source omitted] - Access to secretsline 133
[Credential-related source omitted] - Access to secretsline 134
[Credential-related source omitted] - Access to secretsline 134
[Credential-related source omitted] - Access to secretsline 135
[Credential-related source omitted] - Access to secretsline 135
[Credential-related source omitted] - Access to secretsline 156
[Credential-related source omitted] - Access to secretsline 156
[Credential-related source omitted]
skills/galaxy-bridge/galaxy_catalog.json
- Network accessline 2
"version": "1.0.0", "generated_by": "generate_galaxy_catalog.py", "galaxy_url": "https://usegalaxy.org", - Network accessline 2
"version": "1.0.0", "generated_by": "generate_galaxy_catalog.py", "galaxy_url": "https://usegalaxy.org", - Network accessline 3
"generated_by": "generate_galaxy_catalog.py", "galaxy_url": "https://usegalaxy.org", "generated_at": "2026-03-07T19:50:30.864391+00:00", - Network accessline 3
"generated_by": "generate_galaxy_catalog.py", "galaxy_url": "https://usegalaxy.org", "generated_at": "2026-03-07T19:50:30.864391+00:00", - Network accessline 4
"galaxy_url": "https://usegalaxy.org", - Network accessline 4
"galaxy_url": "https://usegalaxy.org",
skills/galaxy-bridge/generate_curated_skills.py
skills/galaxy-bridge/generate_galaxy_catalog.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 9
Usage: python generate_galaxy_catalog.py # fetch from usegalaxy.org python generate_galaxy_catalog.py --url https://usegalaxy.eu # alternate server - Network accessline 9
Usage: python generate_galaxy_catalog.py # fetch from usegalaxy.org python generate_galaxy_catalog.py --url https://usegalaxy.eu # alternate server - Network accessline 11
python generate_galaxy_catalog.py --url https://usegalaxy.eu # alternate server - Network accessline 11
python generate_galaxy_catalog.py --url https://usegalaxy.eu # alternate server - Network accessline 27
DEFAULT_URL = "https://usegalaxy.org" - Network accessline 27
DEFAULT_URL = "https://usegalaxy.org" - Network accessline 38
api_url = f"{galaxy_url.rstrip('/')}/api/tools?in_panel=false" print(f"Fetching tools from {api_url} ...") resp = requests.get(api_url, timeout=120) - Network accessline 38
api_url = f"{galaxy_url.rstrip('/')}/api/tools?in_panel=false" print(f"Fetching tools from {api_url} ...") resp = requests.get(api_url, timeout=120) - Network accessline 39
print(f"Fetching tools from {api_url} ...") resp = requests.get(api_url, timeout=120) resp.raise_for_status() - Network accessline 39
print(f"Fetching tools from {api_url} ...") resp = requests.get(api_url, timeout=120) resp.raise_for_status() - Network accessline 40
resp = requests.get(api_url, timeout=120) - Network accessline 40
resp = requests.get(api_url, timeout=120)
skills/galaxy-bridge/tests/__init__.py
skills/galaxy-bridge/tests/test_galaxy_bridge.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 30
"version": "1.0.0", "generated_by": "test", "galaxy_url": "https://usegalaxy.org", - Network accessline 30
"version": "1.0.0", "generated_by": "test", "galaxy_url": "https://usegalaxy.org", - Network accessline 31
"generated_by": "test", "galaxy_url": "https://usegalaxy.org", "tool_count": 5, - Network accessline 31
"generated_by": "test", "galaxy_url": "https://usegalaxy.org", "tool_count": 5, - Network accessline 32
"galaxy_url": "https://usegalaxy.org", - Network accessline 32
"galaxy_url": "https://usegalaxy.org",
skills/galaxy-bridge/tests/test_tool_recommender.py
skills/galaxy-bridge/tool_recommender.py
skills/genome-compare/SKILL.md
- Network accessline 18
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 20
homepage: https://github.com/ClawBio/ClawBio - Network accessline 20
homepage: https://github.com/ClawBio/ClawBio - Network accessline 57
**George Church** (hu43860C) — the first participant in the [Personal Genome Project](https://pgp.med.harvard.edu/). Professor of Genetics at Harvard Medical School. His 23andMe data (569,226 SNPs, CC0 public domain) is bundled in `data/geo - Network accessline 57
**George Church** (hu43860C) — the first participant in the [Personal Genome Project](https://pgp.med.harvard.edu/). Professor of Genetics at Harvard Medical School. His 23andMe data (569,226 SNPs, CC0 public domain) is bundled in `data/geo
skills/genome-compare/__init__.py
skills/genome-compare/api.py
skills/genome-compare/data/manuel_ancestry.json
- Network accessline 2
"name": "Manuel Corpas", "pgp_uk": "uk6D0CFA", "pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA", - Network accessline 2
"name": "Manuel Corpas", "pgp_uk": "uk6D0CFA", "pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA", - Network accessline 3
"pgp_uk": "uk6D0CFA", "pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA", "source": "23andMe Ancestry Composition", - Network accessline 3
"pgp_uk": "uk6D0CFA", "pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA", "source": "23andMe Ancestry Composition", - Network accessline 4
"pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA", - Network accessline 4
"pgp_uk_url": "https://my.personalgenomes.org.uk/profile/uk6D0CFA",
skills/genome-compare/genome_compare.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 538
lines.append(f"**Reference**: George Church (PGP-1, hu43860C) ") if is_demo: lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") - Network accessline 538
lines.append(f"**Reference**: George Church (PGP-1, hu43860C) ") if is_demo: lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") - Network accessline 539
if is_demo: lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") else: - Network accessline 539
if is_demo: lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") else: - Network accessline 540
lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") - Network accessline 540
lines.append("**Input**: Manuel Corpas ([PGP-UK uk6D0CFA](https://my.personalgenomes.org.uk/profile/uk6D0CFA), Corpasome, demo mode) ") - Network accessline 659
lines.append( "**George Church** (hu43860C) is PGP-1 — the first participant in the " "[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor " - Network accessline 659
lines.append( "**George Church** (hu43860C) is PGP-1 — the first participant in the " "[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor " - Network accessline 660
"**George Church** (hu43860C) is PGP-1 — the first participant in the " "[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor " "of genetics at Harvard Medical School and a pioneer of genomics. His 23an - Network accessline 660
"**George Church** (hu43860C) is PGP-1 — the first participant in the " "[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor " "of genetics at Harvard Medical School and a pioneer of genomics. His 23an - Network accessline 661
"[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor " - Network accessline 661
"[Personal Genome Project](https://pgp.med.harvard.edu/). He is a professor "
skills/genome-compare/tests/test_genome_compare.py
skills/genome-match/SKILL.md
- Network accessline 18
always: false emoji: 💞 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
always: false emoji: 💞 homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
emoji: 💞 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
emoji: 💞 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 20
homepage: https://github.com/ClawBio/ClawBio - Network accessline 20
homepage: https://github.com/ClawBio/ClawBio
skills/genome-match/genome_match.py
skills/geo-fetch/SKILL.md
- Network accessline 77
always: false emoji: "📊" homepage: https://www.ncbi.nlm.nih.gov/geo/ - Network accessline 77
always: false emoji: "📊" homepage: https://www.ncbi.nlm.nih.gov/geo/ - Network accessline 78
emoji: "📊" homepage: https://www.ncbi.nlm.nih.gov/geo/ os: - Network accessline 78
emoji: "📊" homepage: https://www.ncbi.nlm.nih.gov/geo/ os: - Network accessline 79
homepage: https://www.ncbi.nlm.nih.gov/geo/ - Network accessline 79
homepage: https://www.ncbi.nlm.nih.gov/geo/ - Access to secretsline 259
[Credential-related source omitted] - Access to secretsline 259
[Credential-related source omitted] - Network accessline 271
sample,fastq_1,fastq_2,strandedness SRS243343,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_2.fastq.gz,auto - Network accessline 271
sample,fastq_1,fastq_2,strandedness SRS243343,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_2.fastq.gz,auto - Network accessline 272
SRS243343,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_2.fastq.gz,auto - Network accessline 272
SRS243343,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_1.fastq.gz,https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR342/SRR342351/SRR342351_2.fastq.gz,auto - Access to secretsline 329
[Credential-related source omitted] - Access to secretsline 329
[Credential-related source omitted] - Access to secretsline 361
[Credential-related source omitted] - Access to secretsline 361
[Credential-related source omitted] - Network accessline 418
- [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/) and - Network accessline 418
- [NCBI GEO](https://www.ncbi.nlm.nih.gov/geo/) and - Network accessline 419
[E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25501/); the endpoints used. - Network accessline 419
[E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25501/); the endpoints used. - Network accessline 420
- [ENA Portal API](https://www.ebi.ac.uk/ena/portal/api/); FASTQ link resolution. - Network accessline 420
- [ENA Portal API](https://www.ebi.ac.uk/ena/portal/api/); FASTQ link resolution. - Network accessline 421
- [nf-core/rnaseq](https://nf-co.re/rnaseq) and - Network accessline 421
- [nf-core/rnaseq](https://nf-co.re/rnaseq) and - Network accessline 422
[nf-core/scrnaseq](https://nf-co.re/scrnaseq); the samplesheet contracts. - Network accessline 422
[nf-core/scrnaseq](https://nf-co.re/scrnaseq); the samplesheet contracts. - Network accessline 423
- Demo fixture: [GSE30720](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30720), - Network accessline 423
- Demo fixture: [GSE30720](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30720), - Network accessline 424
Arabidopsis thaliana seedling RNA-seq; GEO records are public domain. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 424
Arabidopsis thaliana seedling RNA-seq; GEO records are public domain. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 425
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`geo/`, plus `fastq-download-script/` folded in as - Network accessline 425
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`geo/`, plus `fastq-download-script/` folded in as - Network accessline 426
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`geo/`, plus `fastq-download-script/` folded in as `download-script`), © 2026 UK Dementia Research Institute, MIT. - Network accessline 426
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`geo/`, plus `fastq-download-script/` folded in as `download-script`), © 2026 UK Dementia Research Institute, MIT.
skills/geo-fetch/geo_fetch.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 11
[Credential-related source omitted] - Access to secretsline 11
[Credential-related source omitted] - Access to secretsline 66
[Credential-related source omitted] - Access to secretsline 66
[Credential-related source omitted] - Network accessline 82
p.add_argument("--read-map", metavar="R1,R2") p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " - Network accessline 82
p.add_argument("--read-map", metavar="R1,R2") p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " - Network accessline 83
p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " "because it also retries HTTP 403 and aborts a stalled " - Network accessline 83
p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " "because it also retries HTTP 403 and aborts a stalled " - Network accessline 84
help="download-script transfer tool; curl is the default " - Network accessline 84
help="download-script transfer tool; curl is the default " - Network accessline 220
output_dir, title=f"GEO report — {accession}", source_url=f"[Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession})", - Network accessline 220
output_dir, title=f"GEO report — {accession}", source_url=f"[Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession})", - Network accessline 221
title=f"GEO report — {accession}", source_url=f"[Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession})", sections=sections, - Network accessline 221
title=f"GEO report — {accession}", source_url=f"[Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession})", sections=sections, - Network accessline 222
source_url=f"[Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession})", - Network accessline 222
source_url=f"[Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={accession})",
skills/geo-fetch/geo_fetch_api.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Metadata is retrieved through NCBI E-utilities (db=gds); data files are pulled from the GEO FTP tree at https://ftp.ncbi.nlm.nih.gov/geo/ . - Network accessline 8
Metadata is retrieved through NCBI E-utilities (db=gds); data files are pulled from the GEO FTP tree at https://ftp.ncbi.nlm.nih.gov/geo/ . - Network accessline 9
from the GEO FTP tree at https://ftp.ncbi.nlm.nih.gov/geo/ . - Network accessline 9
from the GEO FTP tree at https://ftp.ncbi.nlm.nih.gov/geo/ . - Network accessline 34
EUTILS = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Network accessline 34
EUTILS = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Network accessline 35
FTP_BASE = "https://ftp.ncbi.nlm.nih.gov/geo" - Network accessline 35
FTP_BASE = "https://ftp.ncbi.nlm.nih.gov/geo" - Network accessline 36
USER_AGENT = "geo-skill/1.0 (https://www.ncbi.nlm.nih.gov/geo/)" - Network accessline 36
USER_AGENT = "geo-skill/1.0 (https://www.ncbi.nlm.nih.gov/geo/)" - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 38
[Credential-related source omitted] - Access to secretsline 42
[Credential-related source omitted] - Access to secretsline 42
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted] - Access to secretsline 43
[Credential-related source omitted] - Access to secretsline 54
[Credential-related source omitted] - Access to secretsline 54
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Network accessline 61
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 61
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 62
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=120) as r: - Network accessline 62
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=120) as r: - Network accessline 63
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 63
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 64
with urllib.request.urlopen(req, timeout=120) as r: - Network accessline 64
with urllib.request.urlopen(req, timeout=120) as r: - Network accessline 192
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 192
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 193
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) size = 0 - Network accessline 193
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) size = 0 - Network accessline 194
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 194
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT}) - Network accessline 195
size = 0 with urllib.request.urlopen(req, timeout=600) as r, open(part, "wb") as fh: try: - Network accessline 195
size = 0 with urllib.request.urlopen(req, timeout=600) as r, open(part, "wb") as fh: try: - Network accessline 196
with urllib.request.urlopen(req, timeout=600) as r, open(part, "wb") as fh: - Network accessline 196
with urllib.request.urlopen(req, timeout=600) as r, open(part, "wb") as fh: - Network accessline 293
ENA_PORTAL = "https://www.ebi.ac.uk/ena/portal/api" - Network accessline 293
ENA_PORTAL = "https://www.ebi.ac.uk/ena/portal/api" - Network accessline 346
`ftp://` is rewritten (these skills never speak FTP), `http(s)://` passes through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 346
`ftp://` is rewritten (these skills never speak FTP), `http(s)://` passes through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 347
through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 347
through, and a scheme-less `host/path` gains `https://`. Anything else, such - Network accessline 517
url = ("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" - Network accessline 517
url = ("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" - Network accessline 759
def geo_sample_soft(gsm): url = ("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" - Network accessline 759
def geo_sample_soft(gsm): url = ("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" - Network accessline 760
url = ("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" - Network accessline 760
url = ("https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" - Access to secretsline 856
[Credential-related source omitted] - Access to secretsline 856
[Credential-related source omitted]
skills/geo-fetch/tests/test_geo_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 33
[Credential-related source omitted] - Access to secretsline 33
[Credential-related source omitted] - Access to secretsline 37
[Credential-related source omitted] - Access to secretsline 37
[Credential-related source omitted] - Access to secretsline 44
[Credential-related source omitted] - Access to secretsline 44
[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Network accessline 67
TO_HTTPS_CASES = [ ("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 67
TO_HTTPS_CASES = [ ("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 68
("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 68
("ftp://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 69
("https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 69
("https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 70
("http://example.org/x.fastq.gz", "http://example.org/x.fastq.gz"), - Network accessline 70
("http://example.org/x.fastq.gz", "http://example.org/x.fastq.gz"), - Network accessline 72
("ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 72
("ftp.sra.ebi.ac.uk/vol1/x.fastq.gz", "https://ftp.sra.ebi.ac.uk/vol1/x.fastq.gz"), - Network accessline 235
body = b"x" * 10_000 with patch.object(api.urllib.request, "urlopen", return_value=_ChunkedResponse(body)): dest = api.download("https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/a.tar", - Network accessline 235
body = b"x" * 10_000 with patch.object(api.urllib.request, "urlopen", return_value=_ChunkedResponse(body)): dest = api.download("https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/a.tar", - Network accessline 236
with patch.object(api.urllib.request, "urlopen", return_value=_ChunkedResponse(body)): dest = api.download("https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/a.tar", str(tmp_path)) - Network accessline 236
with patch.object(api.urllib.request, "urlopen", return_value=_ChunkedResponse(body)): dest = api.download("https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/a.tar", str(tmp_path)) - Network accessline 237
dest = api.download("https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/a.tar", - Network accessline 237
dest = api.download("https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/a.tar", - Network accessline 253
with patch.object(api.urllib.request, "urlopen", side_effect=flaky), \ patch.object(api.time, "sleep"): dest = api.download("https://ftp.ncbi.nlm.nih.gov/x/b.txt", str(tmp_path)) - Network accessline 253
with patch.object(api.urllib.request, "urlopen", side_effect=flaky), \ patch.object(api.time, "sleep"): dest = api.download("https://ftp.ncbi.nlm.nih.gov/x/b.txt", str(tmp_path)) - Network accessline 254
patch.object(api.time, "sleep"): dest = api.download("https://ftp.ncbi.nlm.nih.gov/x/b.txt", str(tmp_path)) assert Path(dest).read_bytes() == b"ok" - Network accessline 254
patch.object(api.time, "sleep"): dest = api.download("https://ftp.ncbi.nlm.nih.gov/x/b.txt", str(tmp_path)) assert Path(dest).read_bytes() == b"ok" - Network accessline 255
dest = api.download("https://ftp.ncbi.nlm.nih.gov/x/b.txt", str(tmp_path)) - Network accessline 255
dest = api.download("https://ftp.ncbi.nlm.nih.gov/x/b.txt", str(tmp_path)) - Network accessline 262
side_effect=AssertionError("must refuse before any request")): with pytest.raises(SystemExit, match="outside"): api.download("https://ftp.ncbi.nlm.nih.gov/x/..", str(tmp_path / "out")) - Network accessline 262
side_effect=AssertionError("must refuse before any request")): with pytest.raises(SystemExit, match="outside"): api.download("https://ftp.ncbi.nlm.nih.gov/x/..", str(tmp_path / "out")) - Network accessline 264
api.download("https://ftp.ncbi.nlm.nih.gov/x/..", str(tmp_path / "out")) - Network accessline 264
api.download("https://ftp.ncbi.nlm.nih.gov/x/..", str(tmp_path / "out")) - Network accessline 272
URL = "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/GSE1_RAW.tar" - Network accessline 272
URL = "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE1nnn/GSE1/suppl/GSE1_RAW.tar"
skills/gi-annotation/SKILL.md
- Network accessline 13
always: false emoji: 📜 homepage: https://docs.genomicintelligence.ai - Network accessline 13
always: false emoji: 📜 homepage: https://docs.genomicintelligence.ai - Network accessline 14
emoji: 📜 homepage: https://docs.genomicintelligence.ai os: - Network accessline 14
emoji: 📜 homepage: https://docs.genomicintelligence.ai os: - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 82
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 82
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 105
`POST https://api.genomicintelligence.ai/v1/tasks/annotation/predict` with `Prefer: respond-async`. The API accepts either delivery mode on every task; this skill always submits async because the pipeline is long-running. The pipeline strea - Network accessline 105
`POST https://api.genomicintelligence.ai/v1/tasks/annotation/predict` with `Prefer: respond-async`. The API accepts either delivery mode on every task; this skill always submits async because the pipeline is long-running. The pipeline strea - Network accessline 107
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Network accessline 107
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Access to secretsline 131
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Access to secretsline 134
[Credential-related source omitted] - Access to secretsline 134
[Credential-related source omitted] - Access to secretsline 143
[Credential-related source omitted] - Access to secretsline 143
[Credential-related source omitted] - Access to secretsline 144
[Credential-related source omitted] - Access to secretsline 144
[Credential-related source omitted] - Access to secretsline 152
[Credential-related source omitted] - Access to secretsline 152
[Credential-related source omitted]
skills/gi-annotation/api.py
skills/gi-annotation/gi_annotation.py
skills/gi-annotation/tests/__init__.py
skills/gi-annotation/tests/test_gi_annotation.py
skills/gi-chromatin/SKILL.md
- Network accessline 12
always: false emoji: 🧶 homepage: https://docs.genomicintelligence.ai - Network accessline 12
always: false emoji: 🧶 homepage: https://docs.genomicintelligence.ai - Network accessline 13
emoji: 🧶 homepage: https://docs.genomicintelligence.ai os: - Network accessline 13
emoji: 🧶 homepage: https://docs.genomicintelligence.ai os: - Network accessline 14
homepage: https://docs.genomicintelligence.ai - Network accessline 14
homepage: https://docs.genomicintelligence.ai - Network accessline 85
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 85
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 109
`POST https://api.genomicintelligence.ai/v1/tasks/chromatin/predict`. Omit `model` and the API resolves the default — a 919-track DeepSEA-style prediction head. `GET /v1/tasks/chromatin/models` is the current list. - Network accessline 109
`POST https://api.genomicintelligence.ai/v1/tasks/chromatin/predict`. Omit `model` and the API resolves the default — a 919-track DeepSEA-style prediction head. `GET /v1/tasks/chromatin/models` is the current list. - Network accessline 111
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Network accessline 111
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Access to secretsline 141
[Credential-related source omitted] - Access to secretsline 141
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Access to secretsline 150
[Credential-related source omitted] - Access to secretsline 150
[Credential-related source omitted] - Access to secretsline 168
[Credential-related source omitted] - Access to secretsline 168
[Credential-related source omitted]
skills/gi-chromatin/api.py
skills/gi-chromatin/gi_chromatin.py
skills/gi-chromatin/tests/__init__.py
skills/gi-chromatin/tests/test_gi_chromatin.py
skills/gi-enhancer/SKILL.md
- Network accessline 12
always: false emoji: 🎚<U+FE0F> homepage: https://docs.genomicintelligence.ai - Network accessline 12
always: false emoji: 🎚<U+FE0F> homepage: https://docs.genomicintelligence.ai - Network accessline 13
emoji: 🎚<U+FE0F> homepage: https://docs.genomicintelligence.ai os: - Network accessline 13
emoji: 🎚<U+FE0F> homepage: https://docs.genomicintelligence.ai os: - Network accessline 14
homepage: https://docs.genomicintelligence.ai - Network accessline 14
homepage: https://docs.genomicintelligence.ai - Network accessline 82
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 82
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 106
`POST https://api.genomicintelligence.ai/v1/tasks/enhancer/predict`. Omit `model` and the API resolves the default — a DeepSTARR model trained on *Drosophila* S2 cells. `GET /v1/tasks/enhancer/models` is the current list. - Network accessline 106
`POST https://api.genomicintelligence.ai/v1/tasks/enhancer/predict`. Omit `model` and the API resolves the default — a DeepSTARR model trained on *Drosophila* S2 cells. `GET /v1/tasks/enhancer/models` is the current list. - Network accessline 108
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Network accessline 108
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Access to secretsline 126
[Credential-related source omitted] - Access to secretsline 126
[Credential-related source omitted] - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 129
[Credential-related source omitted] - Access to secretsline 138
[Credential-related source omitted] - Access to secretsline 138
[Credential-related source omitted] - Access to secretsline 139
[Credential-related source omitted] - Access to secretsline 139
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 164
[Credential-related source omitted] - Access to secretsline 164
[Credential-related source omitted]
skills/gi-enhancer/api.py
skills/gi-enhancer/gi_enhancer.py
skills/gi-enhancer/tests/__init__.py
skills/gi-enhancer/tests/test_gi_enhancer.py
skills/gi-expression/SKILL.md
- Network accessline 13
always: false emoji: 🧪 homepage: https://docs.genomicintelligence.ai - Network accessline 13
always: false emoji: 🧪 homepage: https://docs.genomicintelligence.ai - Network accessline 14
emoji: 🧪 homepage: https://docs.genomicintelligence.ai os: - Network accessline 14
emoji: 🧪 homepage: https://docs.genomicintelligence.ai os: - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 81
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 81
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 104
`POST https://api.genomicintelligence.ai/v1/tasks/expression/predict`. Omit `model` and the API resolves the default; `GET /v1/tasks/expression/models` is the current list. - Network accessline 104
`POST https://api.genomicintelligence.ai/v1/tasks/expression/predict`. Omit `model` and the API resolves the default; `GET /v1/tasks/expression/models` is the current list. - Network accessline 106
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Network accessline 106
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Access to secretsline 139
[Credential-related source omitted] - Access to secretsline 139
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Access to secretsline 151
[Credential-related source omitted] - Access to secretsline 151
[Credential-related source omitted] - Access to secretsline 152
[Credential-related source omitted] - Access to secretsline 152
[Credential-related source omitted] - Access to secretsline 160
[Credential-related source omitted] - Access to secretsline 160
[Credential-related source omitted] - Access to secretsline 182
[Credential-related source omitted] - Access to secretsline 182
[Credential-related source omitted]
skills/gi-expression/api.py
skills/gi-expression/gi_expression.py
skills/gi-expression/tests/__init__.py
skills/gi-expression/tests/test_gi_expression.py
skills/gi-promoter/SKILL.md
- Network accessline 13
always: false emoji: 🧬 homepage: https://docs.genomicintelligence.ai - Network accessline 13
always: false emoji: 🧬 homepage: https://docs.genomicintelligence.ai - Network accessline 14
emoji: 🧬 homepage: https://docs.genomicintelligence.ai os: - Network accessline 14
emoji: 🧬 homepage: https://docs.genomicintelligence.ai os: - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 82
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 82
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 108
`POST https://api.genomicintelligence.ai/v1/tasks/promoter/predict`. Omit `model` and the API resolves the default — a GENA-LM BERT Large transformer with a 2000 bp context and a 1000 bp prediction window. Shorter-context and DNABERT varian - Network accessline 108
`POST https://api.genomicintelligence.ai/v1/tasks/promoter/predict`. Omit `model` and the API resolves the default — a GENA-LM BERT Large transformer with a 2000 bp context and a 1000 bp prediction window. Shorter-context and DNABERT varian - Network accessline 110
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Network accessline 110
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Access to secretsline 144
[Credential-related source omitted] - Access to secretsline 144
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 156
[Credential-related source omitted] - Access to secretsline 156
[Credential-related source omitted] - Access to secretsline 157
[Credential-related source omitted] - Access to secretsline 157
[Credential-related source omitted] - Access to secretsline 165
[Credential-related source omitted] - Access to secretsline 165
[Credential-related source omitted] - Access to secretsline 175
[Credential-related source omitted] - Access to secretsline 175
[Credential-related source omitted]
skills/gi-promoter/api.py
skills/gi-promoter/gi_promoter.py
skills/gi-promoter/tests/__init__.py
skills/gi-promoter/tests/test_gi_promoter.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 3
Marked ``integration`` because the demo hits the real GI API (https://api.genomicintelligence.ai). - Network accessline 3
Marked ``integration`` because the demo hits the real GI API (https://api.genomicintelligence.ai).
skills/gi-splice/SKILL.md
- Network accessline 13
always: false emoji: ✂<U+FE0F> homepage: https://docs.genomicintelligence.ai - Network accessline 13
always: false emoji: ✂<U+FE0F> homepage: https://docs.genomicintelligence.ai - Network accessline 14
emoji: ✂<U+FE0F> homepage: https://docs.genomicintelligence.ai os: - Network accessline 14
emoji: ✂<U+FE0F> homepage: https://docs.genomicintelligence.ai os: - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 15
homepage: https://docs.genomicintelligence.ai - Network accessline 83
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 83
> ⚠<U+FE0F> **Remote inference — opt-in required.** Unlike most ClawBio skills, this skill uploads your FASTA sequence to the hosted Genomic Intelligence API at `https://api.genomicintelligence.ai`. The same models also run interactively at <https - Network accessline 107
`POST https://api.genomicintelligence.ai/v1/tasks/splice/predict`. Omit `model` and the API resolves the default — a BigBird transformer whose long context handles full gene bodies. `GET /v1/tasks/splice/models` is the current list. - Network accessline 107
`POST https://api.genomicintelligence.ai/v1/tasks/splice/predict`. Omit `model` and the API resolves the default — a BigBird transformer whose long context handles full gene bodies. `GET /v1/tasks/splice/models` is the current list. - Network accessline 109
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Network accessline 109
> **Contract note.** The Genomic Intelligence API publishes one operation per task, each with its own request schema: per-task `minLength`/`maxLength` on `sequence`, and a typed, closed `options` object (an unknown option key is a `422 vali - Access to secretsline 140
[Credential-related source omitted] - Access to secretsline 140
[Credential-related source omitted] - Access to secretsline 143
[Credential-related source omitted] - Access to secretsline 143
[Credential-related source omitted] - Access to secretsline 152
[Credential-related source omitted] - Access to secretsline 152
[Credential-related source omitted] - Access to secretsline 153
[Credential-related source omitted] - Access to secretsline 153
[Credential-related source omitted] - Access to secretsline 161
[Credential-related source omitted] - Access to secretsline 161
[Credential-related source omitted] - Access to secretsline 173
[Credential-related source omitted] - Access to secretsline 173
[Credential-related source omitted]
skills/gi-splice/gi_splice.py
skills/gi-splice/tests/__init__.py
skills/gi-splice/tests/test_gi_splice.py
skills/gwas-catalog-region-fetch/SKILL.md
- Network accessline 51
- examples/input.json endpoints: - https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # tabix-on-FTP harmonised - Network accessline 51
- examples/input.json endpoints: - https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # tabix-on-FTP harmonised - Network accessline 52
endpoints: - https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # tabix-on-FTP harmonised openclaw: - Network accessline 52
endpoints: - https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # tabix-on-FTP harmonised openclaw: - Network accessline 53
- https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # tabix-on-FTP harmonised - Network accessline 53
- https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # tabix-on-FTP harmonised - Network accessline 61
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 61
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 62
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 62
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 63
homepage: https://github.com/ClawBio/ClawBio - Network accessline 63
homepage: https://github.com/ClawBio/ClawBio - Network accessline 83
The NHGRI-EBI GWAS Catalog (Sollis 2023 *NAR*) maintains harmonised summary statistics for ~25,000 published GWAS at `https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST>/harmonised/<GCST>.h.tsv.gz`. The harmonisation pipeline - Network accessline 83
The NHGRI-EBI GWAS Catalog (Sollis 2023 *NAR*) maintains harmonised summary statistics for ~25,000 published GWAS at `https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST>/harmonised/<GCST>.h.tsv.gz`. The harmonisation pipeline - Network accessline 110
1. **Resolve `accession`**: the canonical `GCST########` identifier. Look up via the GWAS Catalog REST API v2 (`https://www.ebi.ac.uk/gwas/rest/api/v2/studies/<GCST>`; the legacy v1 `/gwas/rest/api/studies/` path is retired and returns HTTP - Network accessline 110
1. **Resolve `accession`**: the canonical `GCST########` identifier. Look up via the GWAS Catalog REST API v2 (`https://www.ebi.ac.uk/gwas/rest/api/v2/studies/<GCST>`; the legacy v1 `/gwas/rest/api/studies/` path is retired and returns HTTP - Network accessline 185
accession: GCST90269602 harmonised_path: GCST90269602/harmonised/GCST90269602.h.tsv.gz source_url: https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90269602/harmonised/GCST90269602.h.tsv.gz - Network accessline 185
accession: GCST90269602 harmonised_path: GCST90269602/harmonised/GCST90269602.h.tsv.gz source_url: https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90269602/harmonised/GCST90269602.h.tsv.gz - Network accessline 186
harmonised_path: GCST90269602/harmonised/GCST90269602.h.tsv.gz source_url: https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90269602/harmonised/GCST90269602.h.tsv.gz fetched_at_utc: '2026-05-09T11:42:06Z' - Network accessline 186
harmonised_path: GCST90269602/harmonised/GCST90269602.h.tsv.gz source_url: https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90269602/harmonised/GCST90269602.h.tsv.gz fetched_at_utc: '2026-05-09T11:42:06Z' - Network accessline 187
source_url: https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90269602/harmonised/GCST90269602.h.tsv.gz - Network accessline 187
source_url: https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90269602/harmonised/GCST90269602.h.tsv.gz
skills/gwas-catalog-region-fetch/examples/run_example.sh
skills/gwas-catalog-region-fetch/gwas_catalog_region_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 7
Source layout: - Per-study harmonised TSV.bgz at https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST_PREFIX>/<GCST>/harmonised/ - Network accessline 7
Source layout: - Per-study harmonised TSV.bgz at https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST_PREFIX>/<GCST>/harmonised/ - Network accessline 8
- Per-study harmonised TSV.bgz at https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST_PREFIX>/<GCST>/harmonised/ with a sibling .tbi tabix index. - Network accessline 8
- Per-study harmonised TSV.bgz at https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST_PREFIX>/<GCST>/harmonised/ with a sibling .tbi tabix index. - Network accessline 9
https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST_PREFIX>/<GCST>/harmonised/ - Network accessline 9
https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/<GCST_PREFIX>/<GCST>/harmonised/ - Network accessline 54
DEFAULT_FTP_BASE = "https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics" - Network accessline 54
DEFAULT_FTP_BASE = "https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics" - Network accessline 60
"""Records the GWAS Catalog mirror release pinned per fetch (for the manifest).""" - Network accessline 60
"""Records the GWAS Catalog mirror release pinned per fetch (for the manifest).""" - Network accessline 153
base = gcst_url_base(accession, ftp_base=ftp_base) sess = session or requests.Session() - Network accessline 153
base = gcst_url_base(accession, ftp_base=ftp_base) sess = session or requests.Session() - Network accessline 154
sess = session or requests.Session() - Network accessline 154
sess = session or requests.Session() - Network accessline 192
self.ftp_base = ftp_base.rstrip("/") self.timeout_s = timeout_s self.session = session or requests.Session() - Network accessline 192
self.ftp_base = ftp_base.rstrip("/") self.timeout_s = timeout_s self.session = session or requests.Session() - Network accessline 194
self.session = session or requests.Session() - Network accessline 194
self.session = session or requests.Session() - Network accessline 259
chrom_q = chromosome.lstrip("chr") try: rows = list(tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp)) - Network accessline 259
chrom_q = chromosome.lstrip("chr") try: rows = list(tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp)) - Network accessline 260
try: rows = list(tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp)) except ValueError as e: - Network accessline 260
try: rows = list(tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp)) except ValueError as e: - Network accessline 261
rows = list(tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp)) - Network accessline 261
rows = list(tbx.fetch(chrom_q, max(0, start_bp - 1), end_bp)) - Network accessline 264
if not chrom_q.startswith("chr"): rows = list(tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp)) - Network accessline 264
if not chrom_q.startswith("chr"): rows = list(tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp)) - Network accessline 265
rows = list(tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp)) - Network accessline 265
rows = list(tbx.fetch(f"chr{chrom_q}", max(0, start_bp - 1), end_bp))
skills/gwas-catalog-region-fetch/tests/conftest.py
skills/gwas-catalog-region-fetch/tests/test_gwas_catalog_region_fetch.py
skills/gwas-catalog-region-fetch/tests/test_live_gwas_catalog_region_fetch.py
skills/gwas-catalog-region-fetch/tests/test_reproducibility_bundle.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 20
)], release=grf.GWASCatalogRelease( accession=cfg["accession"], harmonised_url="https://example.invalid/x.h.tsv.gz", - Network accessline 20
)], release=grf.GWASCatalogRelease( accession=cfg["accession"], harmonised_url="https://example.invalid/x.h.tsv.gz", - Network accessline 21
release=grf.GWASCatalogRelease( accession=cfg["accession"], harmonised_url="https://example.invalid/x.h.tsv.gz", fetched_at_utc="2026-01-01T00:00:00Z", - Network accessline 21
release=grf.GWASCatalogRelease( accession=cfg["accession"], harmonised_url="https://example.invalid/x.h.tsv.gz", fetched_at_utc="2026-01-01T00:00:00Z", - Network accessline 22
accession=cfg["accession"], harmonised_url="https://example.invalid/x.h.tsv.gz", - Network accessline 22
accession=cfg["accession"], harmonised_url="https://example.invalid/x.h.tsv.gz",
skills/gwas-lookup/SKILL.md
- Network accessline 12
always: false emoji: 🔍 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🔍 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🔍 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
emoji: 🔍 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 29
Inspired by [Sasha Gusev's GWAS Lookup](https://sashagusev.github.io/gwas_lookup/). - Network accessline 29
Inspired by [Sasha Gusev's GWAS Lookup](https://sashagusev.github.io/gwas_lookup/).
skills/gwas-lookup/gwas_lookup.py
skills/gwas-lookup/gwas_lookup_api/__init__.py
skills/gwas-lookup/gwas_lookup_api/base_client.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 54
self.session = requests.Session() - Network accessline 54
self.session = requests.Session() - Network accessline 116
if not resp.ok: raise requests.HTTPError( - Network accessline 116
if not resp.ok: raise requests.HTTPError( - Network accessline 117
raise requests.HTTPError( - Network accessline 117
raise requests.HTTPError(
skills/gwas-lookup/gwas_lookup_api/ensembl.py
skills/gwas-lookup/gwas_lookup_api/finngen.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Endpoint: GET https://r12.finngen.fi/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 4
Endpoint: GET https://r12.finngen.fi/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 5
GET https://r12.finngen.fi/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 5
GET https://r12.finngen.fi/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 15
BASE_URL = "https://r12.finngen.fi" - Network accessline 15
BASE_URL = "https://r12.finngen.fi"
skills/gwas-lookup/gwas_lookup_api/gtex.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Endpoint: GET https://gtexportal.org/api/v2/association/singleTissueEqtl - Network accessline 4
Endpoint: GET https://gtexportal.org/api/v2/association/singleTissueEqtl - Network accessline 5
GET https://gtexportal.org/api/v2/association/singleTissueEqtl - Network accessline 5
GET https://gtexportal.org/api/v2/association/singleTissueEqtl - Network accessline 16
BASE_URL = "https://gtexportal.org/api/v2" - Network accessline 16
BASE_URL = "https://gtexportal.org/api/v2"
skills/gwas-lookup/gwas_lookup_api/gwas_catalog.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 7
The legacy v1 API (/gwas/rest/api/singleNucleotidePolymorphisms/...) was retired and answers HTTP 410. See https://www.ebi.ac.uk/gwas/docs/news/rest-api-v2-migration-guide - Network accessline 7
The legacy v1 API (/gwas/rest/api/singleNucleotidePolymorphisms/...) was retired and answers HTTP 410. See https://www.ebi.ac.uk/gwas/docs/news/rest-api-v2-migration-guide - Network accessline 9
https://www.ebi.ac.uk/gwas/docs/news/rest-api-v2-migration-guide - Network accessline 9
https://www.ebi.ac.uk/gwas/docs/news/rest-api-v2-migration-guide - Network accessline 26
BASE_URL = "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 26
BASE_URL = "https://www.ebi.ac.uk/gwas/rest/api/v2"
skills/gwas-lookup/gwas_lookup_api/open_targets.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Endpoint: POST https://api.platform.opentargets.org/api/v4/graphql - Network accessline 4
Endpoint: POST https://api.platform.opentargets.org/api/v4/graphql - Network accessline 5
POST https://api.platform.opentargets.org/api/v4/graphql - Network accessline 5
POST https://api.platform.opentargets.org/api/v4/graphql - Network accessline 16
BASE_URL = "https://api.platform.opentargets.org/api/v4" - Network accessline 16
BASE_URL = "https://api.platform.opentargets.org/api/v4"
skills/gwas-lookup/gwas_lookup_api/pheweb_bbj.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Endpoint: GET https://pheweb.jp/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 4
Endpoint: GET https://pheweb.jp/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 5
GET https://pheweb.jp/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 5
GET https://pheweb.jp/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 17
BASE_URL = "https://pheweb.jp" - Network accessline 17
BASE_URL = "https://pheweb.jp"
skills/gwas-lookup/gwas_lookup_api/pheweb_ukb.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Endpoint: GET https://pheweb.org/UKB-TOPMed/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 4
Endpoint: GET https://pheweb.org/UKB-TOPMed/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 5
GET https://pheweb.org/UKB-TOPMed/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 5
GET https://pheweb.org/UKB-TOPMed/api/variant/{chr}:{pos}-{ref}-{alt} - Network accessline 15
BASE_URL = "https://pheweb.org/UKB-TOPMed" - Network accessline 15
BASE_URL = "https://pheweb.org/UKB-TOPMed"
skills/gwas-lookup/gwas_lookup_api/portaldev.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 4
Endpoint: GET https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/?q={rsid}&build=GRCh38 - Network accessline 4
Endpoint: GET https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/?q={rsid}&build=GRCh38 - Network accessline 5
GET https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/?q={rsid}&build=GRCh38 - Network accessline 5
GET https://portaldev.sph.umich.edu/api/v1/annotation/omnisearch/?q={rsid}&build=GRCh38 - Network accessline 15
BASE_URL = "https://portaldev.sph.umich.edu/api/v1" - Network accessline 15
BASE_URL = "https://portaldev.sph.umich.edu/api/v1"
skills/gwas-lookup/gwas_lookup_core/__init__.py
skills/gwas-lookup/gwas_lookup_core/normalise.py
skills/gwas-lookup/gwas_lookup_core/report.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 352
"version": "0.2.0", "apis": { "ensembl": "https://rest.ensembl.org", - Network accessline 352
"version": "0.2.0", "apis": { "ensembl": "https://rest.ensembl.org", - Network accessline 353
"apis": { "ensembl": "https://rest.ensembl.org", "gwas_catalog": "https://www.ebi.ac.uk/gwas/rest/api/v2", - Network accessline 353
"apis": { "ensembl": "https://rest.ensembl.org", "gwas_catalog": "https://www.ebi.ac.uk/gwas/rest/api/v2", - Network accessline 354
"ensembl": "https://rest.ensembl.org", - Network accessline 354
"ensembl": "https://rest.ensembl.org", - Network accessline 355
"gwas_catalog": "https://www.ebi.ac.uk/gwas/rest/api/v2", - Network accessline 355
"gwas_catalog": "https://www.ebi.ac.uk/gwas/rest/api/v2", - Network accessline 356
"open_targets": "https://api.platform.opentargets.org/api/v4", - Network accessline 356
"open_targets": "https://api.platform.opentargets.org/api/v4", - Network accessline 357
"pheweb_ukb": "https://pheweb.org/UKB-TOPMed", - Network accessline 357
"pheweb_ukb": "https://pheweb.org/UKB-TOPMed", - Network accessline 358
"finngen": "https://r12.finngen.fi", - Network accessline 358
"finngen": "https://r12.finngen.fi", - Network accessline 359
"pheweb_bbj": "https://pheweb.jp", - Network accessline 359
"pheweb_bbj": "https://pheweb.jp", - Network accessline 360
"gtex": "https://gtexportal.org/api/v2", - Network accessline 360
"gtex": "https://gtexportal.org/api/v2", - Network accessline 361
"portaldev": "https://portaldev.sph.umich.edu/api/v1", - Network accessline 361
"portaldev": "https://portaldev.sph.umich.edu/api/v1",
skills/gwas-lookup/gwas_lookup_core/resolve.py
skills/gwas-lookup/tests/__init__.py
skills/gwas-lookup/tests/fixtures/gwas_catalog_legacy_410.txt
- Network accessline 1
This legacy GWAS Catalog REST API is no longer available. For general programmatic access, see: https://www.ebi.ac.uk/gwas/docs/programmatic-access/ - Network accessline 1
This legacy GWAS Catalog REST API is no longer available. For general programmatic access, see: https://www.ebi.ac.uk/gwas/docs/programmatic-access/ - Network accessline 2
For general programmatic access, see: https://www.ebi.ac.uk/gwas/docs/programmatic-access/ - Network accessline 2
For general programmatic access, see: https://www.ebi.ac.uk/gwas/docs/programmatic-access/ - Network accessline 3
For V2 migration, see: https://www.ebi.ac.uk/gwas/docs/news/rest-api-v2-migration-guide - Network accessline 3
For V2 migration, see: https://www.ebi.ac.uk/gwas/docs/news/rest-api-v2-migration-guide
skills/gwas-lookup/tests/fixtures/gwas_catalog_v2_rs2187668.json
- Network accessline 45
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384" - Network accessline 45
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384" - Network accessline 46
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384" }, - Network accessline 46
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384" }, - Network accessline 47
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384" - Network accessline 47
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384" - Network accessline 48
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384/loci" - Network accessline 48
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384/loci" - Network accessline 49
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384/loci" }, - Network accessline 49
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384/loci" }, - Network accessline 50
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384/loci" - Network accessline 50
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/10071384/loci" - Network accessline 51
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 51
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 52
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" } - Network accessline 52
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" } - Network accessline 53
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 53
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 100
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025" - Network accessline 100
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025" - Network accessline 101
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025" }, - Network accessline 101
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025" }, - Network accessline 102
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025" - Network accessline 102
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025" - Network accessline 103
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025/loci" - Network accessline 103
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025/loci" - Network accessline 104
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025/loci" }, - Network accessline 104
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025/loci" }, - Network accessline 105
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025/loci" - Network accessline 105
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/41025/loci" - Network accessline 106
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 106
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 107
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" } - Network accessline 107
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" } - Network accessline 108
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 108
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs2187668" - Network accessline 153
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/188349641" - Network accessline 153
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/188349641" - Network accessline 154
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"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/19284148/loci" }, - Network accessline 8108
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/19284148/loci" }, - Network accessline 8109
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/19284148/loci" - Network accessline 8109
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/19284148/loci" - Network accessline 8110
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8110
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8111
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" } - Network accessline 8111
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" } - Network accessline 8112
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8112
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8161
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433" - Network accessline 8161
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433" - Network accessline 8162
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433" }, - Network accessline 8162
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433" }, - Network accessline 8163
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433" - Network accessline 8163
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433" - Network accessline 8164
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433/loci" - Network accessline 8164
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433/loci" - Network accessline 8165
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433/loci" }, - Network accessline 8165
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433/loci" }, - Network accessline 8166
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433/loci" - Network accessline 8166
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/27281433/loci" - Network accessline 8167
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8167
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8168
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" } - Network accessline 8168
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" } - Network accessline 8169
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8169
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8214
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438" - Network accessline 8214
"_links": { "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438" - Network accessline 8215
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438" }, - Network accessline 8215
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438" }, - Network accessline 8216
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438" - Network accessline 8216
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438" - Network accessline 8217
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438/loci" - Network accessline 8217
}, "loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438/loci" - Network accessline 8218
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438/loci" }, - Network accessline 8218
"loci": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438/loci" }, - Network accessline 8219
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438/loci" - Network accessline 8219
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations/21314438/loci" - Network accessline 8220
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8220
}, "snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8221
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" } - Network accessline 8221
"snp": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" } - Network accessline 8222
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8222
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/single-nucleotide-polymorphisms/rs7903146" - Network accessline 8228
"_links": { "first": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8228
"_links": { "first": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8229
"first": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" }, - Network accessline 8229
"first": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" }, - Network accessline 8230
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8230
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8231
}, "prev": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8231
}, "prev": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8232
"prev": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" }, - Network accessline 8232
"prev": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" }, - Network accessline 8233
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8233
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=0&size=200&sort=p_value" - Network accessline 8234
}, "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" - Network accessline 8234
}, "self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" - Network accessline 8235
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" }, - Network accessline 8235
"self": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" }, - Network accessline 8236
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" - Network accessline 8236
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" - Network accessline 8237
}, "last": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" - Network accessline 8237
}, "last": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" - Network accessline 8238
"last": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" } - Network accessline 8238
"last": { "href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" } - Network accessline 8239
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value" - Network accessline 8239
"href": "https://www.ebi.ac.uk/gwas/rest/api/v2/associations?rs_id=rs7903146&direction=asc&page=1&size=200&sort=p_value"
skills/gwas-lookup/tests/test_base_client.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 51
def _client(server): return BaseClient(f"http://127.0.0.1:{server.server_port}", rate_interval=0.01) - Network accessline 51
def _client(server): return BaseClient(f"http://127.0.0.1:{server.server_port}", rate_interval=0.01) - Network accessline 52
return BaseClient(f"http://127.0.0.1:{server.server_port}", rate_interval=0.01) - Network accessline 52
return BaseClient(f"http://127.0.0.1:{server.server_port}", rate_interval=0.01)
skills/gwas-lookup/tests/test_gwas_catalog_v2.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 59
def test_base_url_is_v2(): assert gwas_catalog.BASE_URL == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 59
def test_base_url_is_v2(): assert gwas_catalog.BASE_URL == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 60
assert gwas_catalog.BASE_URL == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 60
assert gwas_catalog.BASE_URL == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 179
def _response(status: int, body: str) -> requests.Response: resp = requests.Response() - Network accessline 179
def _response(status: int, body: str) -> requests.Response: resp = requests.Response() - Network accessline 180
resp = requests.Response() - Network accessline 180
resp = requests.Response() - Network accessline 181
resp.status_code = status resp._content = body.encode() resp.url = "https://www.ebi.ac.uk/gwas/rest/api/v2/associations" - Network accessline 181
resp.status_code = status resp._content = body.encode() resp.url = "https://www.ebi.ac.uk/gwas/rest/api/v2/associations" - Network accessline 182
resp._content = body.encode() resp.url = "https://www.ebi.ac.uk/gwas/rest/api/v2/associations" resp.reason = "Gone" if status == 410 else "Error" - Network accessline 182
resp._content = body.encode() resp.url = "https://www.ebi.ac.uk/gwas/rest/api/v2/associations" resp.reason = "Gone" if status == 410 else "Error" - Network accessline 183
resp.url = "https://www.ebi.ac.uk/gwas/rest/api/v2/associations" - Network accessline 183
resp.url = "https://www.ebi.ac.uk/gwas/rest/api/v2/associations" - Network accessline 199
def get(self, endpoint, params=None): if (params or {}).get("page") == 1: raise requests.HTTPError("503 Service Unavailable") - Network accessline 199
def get(self, endpoint, params=None): if (params or {}).get("page") == 1: raise requests.HTTPError("503 Service Unavailable") - Network accessline 200
if (params or {}).get("page") == 1: raise requests.HTTPError("503 Service Unavailable") return super().get(endpoint, params) - Network accessline 200
if (params or {}).get("page") == 1: raise requests.HTTPError("503 Service Unavailable") return super().get(endpoint, params) - Network accessline 201
raise requests.HTTPError("503 Service Unavailable") - Network accessline 201
raise requests.HTTPError("503 Service Unavailable") - Network accessline 230
write_reproducibility(tmp_path, "python gwas_lookup.py --rsid rs7903146", []) versions = json.loads((tmp_path / "reproducibility" / "api_versions.json").read_text()) assert versions["apis"]["gwas_catalog"] == "https://www.ebi.ac.uk/ - Network accessline 230
write_reproducibility(tmp_path, "python gwas_lookup.py --rsid rs7903146", []) versions = json.loads((tmp_path / "reproducibility" / "api_versions.json").read_text()) assert versions["apis"]["gwas_catalog"] == "https://www.ebi.ac.uk/ - Network accessline 232
assert versions["apis"]["gwas_catalog"] == "https://www.ebi.ac.uk/gwas/rest/api/v2" - Network accessline 232
assert versions["apis"]["gwas_catalog"] == "https://www.ebi.ac.uk/gwas/rest/api/v2"
skills/gwas-lookup/tests/test_gwas_lookup.py
skills/gwas-lookup/tests/test_live_gwas_lookup.py
skills/gwas-pipeline/SKILL.md
- Network accessline 23
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 24
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 142
- [Mbatchou et al. (2021)](https://pubmed.ncbi.nlm.nih.gov/34017140/) — REGENIE: computationally efficient whole-genome regression. *Nature Genetics* 53:1097–1103 - Network accessline 142
- [Mbatchou et al. (2021)](https://pubmed.ncbi.nlm.nih.gov/34017140/) — REGENIE: computationally efficient whole-genome regression. *Nature Genetics* 53:1097–1103 - Network accessline 143
- [Chang et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/25722852/) — Second-generation PLINK. *GigaScience* 4:7 - Network accessline 143
- [Chang et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/25722852/) — Second-generation PLINK. *GigaScience* 4:7 - Network accessline 144
- [Anderson et al. (2010)](https://pubmed.ncbi.nlm.nih.gov/21085122/) — Data quality control in genetic case-control association studies. *Nature Protocols* 5:1564–1573 - Network accessline 144
- [Anderson et al. (2010)](https://pubmed.ncbi.nlm.nih.gov/21085122/) — Data quality control in genetic case-control association studies. *Nature Protocols* 5:1564–1573
skills/gwas-pipeline/example_data/example.bed
skills/gwas-pipeline/example_data/example.bim
skills/gwas-pipeline/example_data/example.fam
skills/gwas-pipeline/gwas_pipeline.py
skills/gwas-pipeline/tests/__init__.py
skills/gwas-pipeline/tests/test_gwas_pipeline.py
skills/gwas-prs/SKILL.md
- Network accessline 11
always: false emoji: 🎯 homepage: https://www.pgscatalog.org - Network accessline 11
always: false emoji: 🎯 homepage: https://www.pgscatalog.org - Network accessline 12
emoji: 🎯 homepage: https://www.pgscatalog.org os: - Network accessline 12
emoji: 🎯 homepage: https://www.pgscatalog.org os: - Network accessline 13
homepage: https://www.pgscatalog.org - Network accessline 13
homepage: https://www.pgscatalog.org - Network accessline 45
2. **Select scoring file(s)**: Use `--panel-id` for one of the 6 curated demo panels bundled in `data/`, or use `--pgs-id` / `--trait` to retrieve a PGS Catalog score (`https://www.pgscatalog.org/rest/`). - Network accessline 45
2. **Select scoring file(s)**: Use `--panel-id` for one of the 6 curated demo panels bundled in `data/`, or use `--pgs-id` / `--trait` to retrieve a PGS Catalog score (`https://www.pgscatalog.org/rest/`). - Network accessline 220
# Search by trait GET https://www.pgscatalog.org/rest/score/search?trait_id=EFO_0001360 - Network accessline 220
# Search by trait GET https://www.pgscatalog.org/rest/score/search?trait_id=EFO_0001360 - Network accessline 221
GET https://www.pgscatalog.org/rest/score/search?trait_id=EFO_0001360 - Network accessline 221
GET https://www.pgscatalog.org/rest/score/search?trait_id=EFO_0001360 - Network accessline 223
# Get scoring file metadata GET https://www.pgscatalog.org/rest/score/PGS000031 - Network accessline 223
# Get scoring file metadata GET https://www.pgscatalog.org/rest/score/PGS000031 - Network accessline 224
GET https://www.pgscatalog.org/rest/score/PGS000031 - Network accessline 224
GET https://www.pgscatalog.org/rest/score/PGS000031 - Network accessline 226
# Download harmonised scoring file GET https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000031/ScoringFiles/Harmonized/PGS000031_hmPOS_GRCh37.txt.gz - Network accessline 226
# Download harmonised scoring file GET https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000031/ScoringFiles/Harmonized/PGS000031_hmPOS_GRCh37.txt.gz - Network accessline 227
GET https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000031/ScoringFiles/Harmonized/PGS000031_hmPOS_GRCh37.txt.gz - Network accessline 227
GET https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000031/ScoringFiles/Harmonized/PGS000031_hmPOS_GRCh37.txt.gz
skills/gwas-prs/generate_curated_scores.py
skills/gwas-prs/gwas_prs.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 52
PGS_API_BASE = "https://www.pgscatalog.org/rest" RATE_LIMIT_INTERVAL = 0.55 # seconds between requests (stay under 2 req/sec) - Network accessline 52
PGS_API_BASE = "https://www.pgscatalog.org/rest" RATE_LIMIT_INTERVAL = 0.55 # seconds between requests (stay under 2 req/sec) - Access to secretsline 226
[Credential-related source omitted] - Access to secretsline 226
[Credential-related source omitted] - Network accessline 253
self.use_cache = use_cache self._last_request_time = 0.0 self.session = requests.Session() - Network accessline 253
self.use_cache = use_cache self._last_request_time = 0.0 self.session = requests.Session() - Network accessline 254
self._last_request_time = 0.0 self.session = requests.Session() self.session.headers.update({ - Network accessline 254
self._last_request_time = 0.0 self.session = requests.Session() self.session.headers.update({ - Network accessline 255
self.session = requests.Session() - Network accessline 255
self.session = requests.Session() - Network accessline 414
URL pattern: https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/{pgs_id}/ - Network accessline 414
URL pattern: https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/{pgs_id}/ - Network accessline 415
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/{pgs_id}/ - Network accessline 415
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/{pgs_id}/ - Network accessline 429
url = ( f"https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/" - Network accessline 429
url = ( f"https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/" - Network accessline 430
f"https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/" - Network accessline 430
f"https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/" - Network accessline 1067
else: lines.append("**Scoring files**: PGS Catalog " "(https://www.pgscatalog.org/)") - Network accessline 1067
else: lines.append("**Scoring files**: PGS Catalog " "(https://www.pgscatalog.org/)") - Network accessline 1068
lines.append("**Scoring files**: PGS Catalog " "(https://www.pgscatalog.org/)") lines.append("") - Network accessline 1068
lines.append("**Scoring files**: PGS Catalog " "(https://www.pgscatalog.org/)") lines.append("") - Network accessline 1069
"(https://www.pgscatalog.org/)") - Network accessline 1069
"(https://www.pgscatalog.org/)")
skills/gwas-prs/gwas_prs_repro_bundle.py
skills/gwas-prs/tests/fixtures/mock_score_metadata.json
- Network accessline 6
"variants_number": 8, "weight_type": "log(OR)", "ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", - Network accessline 6
"variants_number": 8, "weight_type": "log(OR)", "ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", - Network accessline 7
"weight_type": "log(OR)", "ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", "ftp_harmonized_scoring_files": { - Network accessline 7
"weight_type": "log(OR)", "ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", "ftp_harmonized_scoring_files": { - Network accessline 8
"ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", - Network accessline 8
"ftp_scoring_file": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/PGS000013.txt.gz", - Network accessline 9
"ftp_harmonized_scoring_files": { "GRCh37": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" - Network accessline 9
"ftp_harmonized_scoring_files": { "GRCh37": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" - Network accessline 10
"GRCh37": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" }, - Network accessline 10
"GRCh37": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" }, - Network accessline 11
"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" - Network accessline 11
"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz" - Network accessline 12
}, "GRCh38": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz" - Network accessline 12
}, "GRCh38": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz" - Network accessline 13
"GRCh38": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz" } - Network accessline 13
"GRCh38": { "positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz" } - Network accessline 14
"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz" - Network accessline 14
"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh38.txt.gz"
skills/gwas-prs/tests/fixtures/mock_scores_by_trait.json
- Network accessline 9
"variants_number": 8, "ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} - Network accessline 9
"variants_number": 8, "ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} - Network accessline 10
"ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} } - Network accessline 10
"ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} } - Network accessline 11
"GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} - Network accessline 11
"GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000013/ScoringFiles/Harmonized/PGS000013_hmPOS_GRCh37.txt.gz"} - Network accessline 18
"variants_number": 999999, "ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"} - Network accessline 18
"variants_number": 999999, "ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"} - Network accessline 19
"ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"} } - Network accessline 19
"ftp_harmonized_scoring_files": { "GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"} } - Network accessline 20
"GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"} - Network accessline 20
"GRCh37": {"positions": "https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000999/ScoringFiles/Harmonized/PGS000999_hmPOS_GRCh37.txt.gz"}
skills/gwas-prs/tests/test_curated_panel_ids.py
skills/gwas-prs/tests/test_gwas_prs.py
skills/gwas-prs/tests/test_legacy_alias_opt_in.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 34
OFFLINE = {"HTTPS_PROXY": "http://127.0.0.1:9", "HTTP_PROXY": "http://127.0.0.1:9", - Network accessline 34
OFFLINE = {"HTTPS_PROXY": "http://127.0.0.1:9", "HTTP_PROXY": "http://127.0.0.1:9", - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted]
skills/gwas-prs/tests/test_repro_bundle.py
skills/gwas-prs/tests/test_score_provenance.py
skills/gwas-sumstats-harmonize/SKILL.md
- Network accessline 68
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 68
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 69
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 69
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 70
homepage: https://github.com/ClawBio/ClawBio - Network accessline 70
homepage: https://github.com/ClawBio/ClawBio - Network accessline 277
- [Hayhurst et al. 2022, GWAS-SSF summary statistics format](https://doi.org/10.1101/2022.07.15.500230); canonical column conventions - Network accessline 277
- [Hayhurst et al. 2022, GWAS-SSF summary statistics format](https://doi.org/10.1101/2022.07.15.500230); canonical column conventions - Network accessline 278
- [Winkler et al. 2014, Quality control and conduct of genome-wide association meta-analyses](https://doi.org/10.1038/nprot.2014.071); allele alignment and QC practice - Network accessline 278
- [Winkler et al. 2014, Quality control and conduct of genome-wide association meta-analyses](https://doi.org/10.1038/nprot.2014.071); allele alignment and QC practice - Network accessline 279
- [Hemani et al. 2018, MR-Base / TwoSampleMR harmonisation](https://doi.org/10.7554/eLife.34408); palindromic-SNP handling - Network accessline 279
- [Hemani et al. 2018, MR-Base / TwoSampleMR harmonisation](https://doi.org/10.7554/eLife.34408); palindromic-SNP handling - Network accessline 280
- [Mölder et al. 2021, Sustainable data analysis with Snakemake](https://doi.org/10.12688/f1000research.29032.2); workflow engine - Network accessline 280
- [Mölder et al. 2021, Sustainable data analysis with Snakemake](https://doi.org/10.12688/f1000research.29032.2); workflow engine
skills/gwas-sumstats-harmonize/examples/make_demo_data.py
skills/gwas-sumstats-harmonize/gwas_sumstats_harmonize.py
skills/gwas-sumstats-harmonize/tests/test_gwas_sumstats_harmonize.py
skills/gwas-sumstats-harmonize/workflow/config/config_loader.py
skills/gwas-sumstats-harmonize/workflow/scripts/align_reference.py
skills/gwas-sumstats-harmonize/workflow/scripts/derive_effects.py
skills/gwas-sumstats-harmonize/workflow/scripts/lib/harmonize_lib.py
skills/gwas-sumstats-harmonize/workflow/scripts/map_columns.py
skills/gwas-sumstats-harmonize/workflow/scripts/qc_filter.py
skills/hla-typing/SKILL.md
- Network accessline 44
- python3 always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 44
- python3 always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 45
always: false homepage: https://github.com/ClawBio/ClawBio emoji: 🧬 - Network accessline 45
always: false homepage: https://github.com/ClawBio/ClawBio emoji: 🧬 - Network accessline 46
homepage: https://github.com/ClawBio/ClawBio - Network accessline 46
homepage: https://github.com/ClawBio/ClawBio
skills/hla-typing/api.py
skills/hla-typing/hla_typing.py
skills/hla-typing/tests/test_hla_typing.py
skills/igv-validator/GUIDE.md
skills/igv-validator/SKILL.md
- Network accessline 92
always: false emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 92
always: false emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 93
emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 93
emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 94
homepage: https://github.com/ClawBio/ClawBio - Network accessline 94
homepage: https://github.com/ClawBio/ClawBio - Network accessline 439
- [IGV desktop](https://igv.org/doc/desktop/); Robinson et al., *Nat Biotechnol* 2011: viewer and batch commands - Network accessline 439
- [IGV desktop](https://igv.org/doc/desktop/); Robinson et al., *Nat Biotechnol* 2011: viewer and batch commands - Network accessline 440
- [pysam](https://github.com/pysam-developers/pysam): htslib bindings used for counting - Network accessline 440
- [pysam](https://github.com/pysam-developers/pysam): htslib bindings used for counting - Network accessline 442
- [VCF 4.3 specification](https://samtools.github.io/hts-specs/VCFv4.3.pdf): BND and symbolic SV notation - Network accessline 442
- [VCF 4.3 specification](https://samtools.github.io/hts-specs/VCFv4.3.pdf): BND and symbolic SV notation
skills/igv-validator/demo/make_demo_data.py
skills/igv-validator/igv_validator.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 489
k = min(n1, 20) clip = q[-n1:][:k] alt_seq = (ins + fa.fetch(v.chrom, pos + (L if size < 0 else 0), pos + (L if size < 0 else 0) + k))[:k] - Network accessline 489
k = min(n1, 20) clip = q[-n1:][:k] alt_seq = (ins + fa.fetch(v.chrom, pos + (L if size < 0 else 0), pos + (L if size < 0 else 0) + k))[:k] - Network accessline 490
clip = q[-n1:][:k] alt_seq = (ins + fa.fetch(v.chrom, pos + (L if size < 0 else 0), pos + (L if size < 0 else 0) + k))[:k] ref_seq = fa.fetch(v.chrom, pos, pos + k) - Network accessline 490
clip = q[-n1:][:k] alt_seq = (ins + fa.fetch(v.chrom, pos + (L if size < 0 else 0), pos + (L if size < 0 else 0) + k))[:k] ref_seq = fa.fetch(v.chrom, pos, pos + k) - Network accessline 491
alt_seq = (ins + fa.fetch(v.chrom, pos + (L if size < 0 else 0), pos + (L if size < 0 else 0) + k))[:k] - Network accessline 491
alt_seq = (ins + fa.fetch(v.chrom, pos + (L if size < 0 else 0), pos + (L if size < 0 else 0) + k))[:k] - Network accessline 492
ref_seq = fa.fetch(v.chrom, pos, pos + k) - Network accessline 492
ref_seq = fa.fetch(v.chrom, pos, pos + k) - Network accessline 494
k = min(n0, 20) clip = q[:n0][-k:] alt_seq = (fa.fetch(v.chrom, max(0, pos - k), pos) + ins)[-k:] - Network accessline 494
k = min(n0, 20) clip = q[:n0][-k:] alt_seq = (fa.fetch(v.chrom, max(0, pos - k), pos) + ins)[-k:] - Network accessline 495
clip = q[:n0][-k:] alt_seq = (fa.fetch(v.chrom, max(0, pos - k), pos) + ins)[-k:] ref_seq = fa.fetch(v.chrom, max(0, pos + (L if size < 0 else 0) - k), pos + (L if size < 0 else 0)) - Network accessline 495
clip = q[:n0][-k:] alt_seq = (fa.fetch(v.chrom, max(0, pos - k), pos) + ins)[-k:] ref_seq = fa.fetch(v.chrom, max(0, pos + (L if size < 0 else 0) - k), pos + (L if size < 0 else 0)) - Network accessline 496
alt_seq = (fa.fetch(v.chrom, max(0, pos - k), pos) + ins)[-k:] - Network accessline 496
alt_seq = (fa.fetch(v.chrom, max(0, pos - k), pos) + ins)[-k:] - Network accessline 497
ref_seq = fa.fetch(v.chrom, max(0, pos + (L if size < 0 else 0) - k), pos + (L if size < 0 else 0)) - Network accessline 497
ref_seq = fa.fetch(v.chrom, max(0, pos + (L if size < 0 else 0) - k), pos + (L if size < 0 else 0)) - Network accessline 510
return dlen > 0 or (ins is not None and len(got) == len(ins) and got in ins + ins) if ins is not None: # insertion: the bases between the two places mid = fa.fetch(chrom, lo, hi).upper() - Network accessline 510
return dlen > 0 or (ins is not None and len(got) == len(ins) and got in ins + ins) if ins is not None: # insertion: the bases between the two places mid = fa.fetch(chrom, lo, hi).upper() - Network accessline 511
if ins is not None: # insertion: the bases between the two places mid = fa.fetch(chrom, lo, hi).upper() return ins + mid == mid + got if pos < rp else mid + ins == got + mid - Network accessline 511
if ins is not None: # insertion: the bases between the two places mid = fa.fetch(chrom, lo, hi).upper() return ins + mid == mid + got if pos < rp else mid + ins == got + mid - Network accessline 512
mid = fa.fetch(chrom, lo, hi).upper() - Network accessline 512
mid = fa.fetch(chrom, lo, hi).upper() - Network accessline 515
return fa.fetch(chrom, lo + dlen, hi + dlen).upper() == fa.fetch(chrom, lo, hi).upper() - Network accessline 515
return fa.fetch(chrom, lo + dlen, hi + dlen).upper() == fa.fetch(chrom, lo, hi).upper() - Network accessline 526
for r in bam.fetch(v.chrom, max(0, pos - 1), pos + abs(size) + 1): - Network accessline 526
for r in bam.fetch(v.chrom, max(0, pos - 1), pos + abs(size) + 1): - Network accessline 563
split, disc, depth = set(), set(), set() # all three as read names: one DNA fragment counts once same_chrom = chrom2 == chrom for r in bam.fetch(chrom, max(0, pos - SPLIT_WINDOW), pos + SPLIT_WINDOW): - Network accessline 563
split, disc, depth = set(), set(), set() # all three as read names: one DNA fragment counts once same_chrom = chrom2 == chrom for r in bam.fetch(chrom, max(0, pos - SPLIT_WINDOW), pos + SPLIT_WINDOW): - Network accessline 564
same_chrom = chrom2 == chrom for r in bam.fetch(chrom, max(0, pos - SPLIT_WINDOW), pos + SPLIT_WINDOW): if not _ok(r): - Network accessline 564
same_chrom = chrom2 == chrom for r in bam.fetch(chrom, max(0, pos - SPLIT_WINDOW), pos + SPLIT_WINDOW): if not _ok(r): - Network accessline 565
for r in bam.fetch(chrom, max(0, pos - SPLIT_WINDOW), pos + SPLIT_WINDOW): - Network accessline 565
for r in bam.fetch(chrom, max(0, pos - SPLIT_WINDOW), pos + SPLIT_WINDOW): - Network accessline 734
def _free_port() -> int: with socket.socket() as s: - Network accessline 734
def _free_port() -> int: with socket.socket() as s: - Network accessline 735
with socket.socket() as s: - Network accessline 735
with socket.socket() as s: - Network accessline 793
def _connect(self): s = socket.create_connection(("127.0.0.1", self.port), timeout=5) - Network accessline 793
def _connect(self): s = socket.create_connection(("127.0.0.1", self.port), timeout=5) - Network accessline 794
s = socket.create_connection(("127.0.0.1", self.port), timeout=5) - Network accessline 794
s = socket.create_connection(("127.0.0.1", self.port), timeout=5) - Network accessline 845
for _ in range(15): try: socket.create_connection(("127.0.0.1", self.port), timeout=1).close() - Network accessline 845
for _ in range(15): try: socket.create_connection(("127.0.0.1", self.port), timeout=1).close() - Network accessline 846
try: socket.create_connection(("127.0.0.1", self.port), timeout=1).close() time.sleep(1) - Network accessline 846
try: socket.create_connection(("127.0.0.1", self.port), timeout=1).close() time.sleep(1) - Network accessline 847
socket.create_connection(("127.0.0.1", self.port), timeout=1).close() - Network accessline 847
socket.create_connection(("127.0.0.1", self.port), timeout=1).close() - Network accessline 1366
n = max(1, (end - start + 1) // binsize) # complete bins only: a partial last bin would look like a dip good, allq, lens = [0] * n, [0] * n, [] for r in bam.fetch(chrom, max(0, start - 1), end): - Network accessline 1366
n = max(1, (end - start + 1) // binsize) # complete bins only: a partial last bin would look like a dip good, allq, lens = [0] * n, [0] * n, [] for r in bam.fetch(chrom, max(0, start - 1), end): - Network accessline 1367
good, allq, lens = [0] * n, [0] * n, [] for r in bam.fetch(chrom, max(0, start - 1), end): if r.is_unmapped or r.is_duplicate or r.is_secondary or r.is_supplementary or r.is_qcfail: - Network accessline 1367
good, allq, lens = [0] * n, [0] * n, [] for r in bam.fetch(chrom, max(0, start - 1), end): if r.is_unmapped or r.is_duplicate or r.is_secondary or r.is_supplementary or r.is_qcfail: - Network accessline 1368
for r in bam.fetch(chrom, max(0, start - 1), end): - Network accessline 1368
for r in bam.fetch(chrom, max(0, start - 1), end): - Dangerous shell operationline 1411
lm, rm = st.median(left), st.median(right) - Dangerous shell operationline 1411
lm, rm = st.median(left), st.median(right) - Dangerous shell operationline 1412
change = math.log2((rm + 0.5) / (lm + 0.5)) - Dangerous shell operationline 1412
change = math.log2((rm + 0.5) / (lm + 0.5)) - Dangerous shell operationline 1424
if abs(rm - lm) < STEP_MIN_SPREAD * (mad(vals[:k], lm) + mad(vals[k:], rm) + 1): - Dangerous shell operationline 1424
if abs(rm - lm) < STEP_MIN_SPREAD * (mad(vals[:k], lm) + mad(vals[k:], rm) + 1): - Network accessline 1563
ambiguous = alt_hits = total = 0 with _open_bam(bam_path, fasta) as bam: for r in bam.fetch(chrom, max(0, gstart - 1), gend): - Network accessline 1563
ambiguous = alt_hits = total = 0 with _open_bam(bam_path, fasta) as bam: for r in bam.fetch(chrom, max(0, gstart - 1), gend): - Network accessline 1564
with _open_bam(bam_path, fasta) as bam: for r in bam.fetch(chrom, max(0, gstart - 1), gend): if r.is_unmapped or r.is_duplicate or r.is_secondary or r.is_supplementary or r.is_qcfail: - Network accessline 1564
with _open_bam(bam_path, fasta) as bam: for r in bam.fetch(chrom, max(0, gstart - 1), gend): if r.is_unmapped or r.is_duplicate or r.is_secondary or r.is_supplementary or r.is_qcfail: - Network accessline 1565
for r in bam.fetch(chrom, max(0, gstart - 1), gend): - Network accessline 1565
for r in bam.fetch(chrom, max(0, gstart - 1), gend):
skills/igv-validator/tests/test_igv_validator.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 296
ok = "<script>const options = {sessionURL: s}\nigv.createBrowser(igvDiv, options)</script>" assert "loadDefaultGenomes: false" in iv.safe_igv_page(ok) for bad in ('<script src="https://cdn.example.org/igv.js"></script>' + ok, - Network accessline 296
ok = "<script>const options = {sessionURL: s}\nigv.createBrowser(igvDiv, options)</script>" assert "loadDefaultGenomes: false" in iv.safe_igv_page(ok) for bad in ('<script src="https://cdn.example.org/igv.js"></script>' + ok, - Network accessline 297
assert "loadDefaultGenomes: false" in iv.safe_igv_page(ok) for bad in ('<script src="https://cdn.example.org/igv.js"></script>' + ok, "<script src=//cdn.example.org/igv.js></script>" + ok, - Network accessline 297
assert "loadDefaultGenomes: false" in iv.safe_igv_page(ok) for bad in ('<script src="https://cdn.example.org/igv.js"></script>' + ok, "<script src=//cdn.example.org/igv.js></script>" + ok, - Network accessline 298
for bad in ('<script src="https://cdn.example.org/igv.js"></script>' + ok, - Network accessline 298
for bad in ('<script src="https://cdn.example.org/igv.js"></script>' + ok, - Network accessline 299
"<script src=//cdn.example.org/igv.js></script>" + ok, '<link rel=stylesheet href="https://cdn.example.org/igv.css">' + ok, "<style>@import url('https://cdn.example.org/igv.css');</style>" + ok, - Network accessline 299
"<script src=//cdn.example.org/igv.js></script>" + ok, '<link rel=stylesheet href="https://cdn.example.org/igv.css">' + ok, "<style>@import url('https://cdn.example.org/igv.css');</style>" + ok, - Network accessline 300
'<link rel=stylesheet href="https://cdn.example.org/igv.css">' + ok, - Network accessline 300
'<link rel=stylesheet href="https://cdn.example.org/igv.css">' + ok, - Network accessline 301
"<style>@import url('https://cdn.example.org/igv.css');</style>" + ok, - Network accessline 301
"<style>@import url('https://cdn.example.org/igv.css');</style>" + ok, - Access to secretsline 856
[Credential-related source omitted] - Access to secretsline 856
[Credential-related source omitted] - Network accessline 858
print("INFO fake IGV: failing to start", flush=True); sys.exit(0) print("INFO [CommandListener] Listening on port %d" % port, flush=True) srv = socket.socket(); srv.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) - Network accessline 858
print("INFO fake IGV: failing to start", flush=True); sys.exit(0) print("INFO [CommandListener] Listening on port %d" % port, flush=True) srv = socket.socket(); srv.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) - Network accessline 859
print("INFO [CommandListener] Listening on port %d" % port, flush=True) srv = socket.socket(); srv.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) srv.bind(("127.0.0.1", port)); srv.listen(5) - Network accessline 859
print("INFO [CommandListener] Listening on port %d" % port, flush=True) srv = socket.socket(); srv.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) srv.bind(("127.0.0.1", port)); srv.listen(5) - Network accessline 860
srv = socket.socket(); srv.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1) - Network accessline 860
srv = socket.socket(); srv.setsockopt(socket.SOL_SOCKET, socket.SO_REUSEADDR, 1)
skills/illumina-bridge/SKILL.md
- Access to secretsline 20
[Credential-related source omitted] - Access to secretsline 20
[Credential-related source omitted] - Network accessline 22
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 22
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 23
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
homepage: https://github.com/ClawBio/ClawBio - Network accessline 24
homepage: https://github.com/ClawBio/ClawBio - Access to secretsline 108
[Credential-related source omitted] - Access to secretsline 108
[Credential-related source omitted] - Network accessline 125
[Credential-related source omitted] - Network accessline 125
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted] - Access to secretsline 125
[Credential-related source omitted] - Network accessline 126
export ILLUMINA_ICA_BASE_URL="https://ica.illumina.com/ica/rest" - Network accessline 126
export ILLUMINA_ICA_BASE_URL="https://ica.illumina.com/ica/rest" - Network accessline 136
`ILLUMINA_ICA_BASE_URL` defaults to `https://ica.illumina.com/ica/rest`. Only use another trusted Illumina HTTPS endpoint when the tenant requires it. - Network accessline 136
`ILLUMINA_ICA_BASE_URL` defaults to `https://ica.illumina.com/ica/rest`. Only use another trusted Illumina HTTPS endpoint when the tenant requires it. - Access to secretsline 173
[Credential-related source omitted] - Access to secretsline 173
[Credential-related source omitted] - Network accessline 206
**Optional**: - `ILLUMINA_ICA_API_KEY` — enables metadata-only ICA enrichment - `ILLUMINA_ICA_BASE_URL` — override the ICA API root with a trusted `https://*.illumina.com` endpoint if needed - Network accessline 206
**Optional**: - `ILLUMINA_ICA_API_KEY` — enables metadata-only ICA enrichment - `ILLUMINA_ICA_BASE_URL` — override the ICA API root with a trusted `https://*.illumina.com` endpoint if needed - Access to secretsline 207
[Credential-related source omitted] - Access to secretsline 207
[Credential-related source omitted] - Network accessline 208
- `ILLUMINA_ICA_BASE_URL` — override the ICA API root with a trusted `https://*.illumina.com` endpoint if needed - Network accessline 208
- `ILLUMINA_ICA_BASE_URL` — override the ICA API root with a trusted `https://*.illumina.com` endpoint if needed - Access to secretsline 214
[Credential-related source omitted] - Access to secretsline 214
[Credential-related source omitted] - Access to secretsline 230
[Credential-related source omitted] - Access to secretsline 230
[Credential-related source omitted] - Network accessline 241
[Credential-related source omitted] - Network accessline 241
[Credential-related source omitted] - Access to secretsline 241
[Credential-related source omitted] - Access to secretsline 241
[Credential-related source omitted] - Network accessline 242
export ILLUMINA_ICA_BASE_URL="https://ica.illumina.com/ica/rest" - Network accessline 242
export ILLUMINA_ICA_BASE_URL="https://ica.illumina.com/ica/rest" - Network accessline 267
- [DRAGEN secondary analysis](https://www.illumina.com/products/by-type/informatics-products/dragen-secondary-analysis.html) - Network accessline 267
- [DRAGEN secondary analysis](https://www.illumina.com/products/by-type/informatics-products/dragen-secondary-analysis.html) - Network accessline 268
- [Illumina Connected Analytics](https://www.illumina.com/products/by-type/informatics-products/connected-analytics.html) - Network accessline 268
- [Illumina Connected Analytics](https://www.illumina.com/products/by-type/informatics-products/connected-analytics.html) - Network accessline 269
- [BCL Convert Sample Sheet](https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/BCLConvert/SampleSheets_swBCL.htm) - Network accessline 269
- [BCL Convert Sample Sheet](https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/BCLConvert/SampleSheets_swBCL.htm) - Network accessline 270
- [ICA public OpenAPI v3 spec](https://ica.illumina.com/ica/api/swagger/openapi_public.yaml) (`info.version: "3"`, server path `/ica/rest`) - Network accessline 270
- [ICA public OpenAPI v3 spec](https://ica.illumina.com/ica/api/swagger/openapi_public.yaml) (`info.version: "3"`, server path `/ica/rest`) - Network accessline 271
- [Issue #74 live ICA validation comment, 2026-09-28](https://github.com/ClawBio/ClawBio/issues/74#issuecomment-5876103282) - Network accessline 271
- [Issue #74 live ICA validation comment, 2026-09-28](https://github.com/ClawBio/ClawBio/issues/74#issuecomment-5876103282) - Network accessline 272
- [Issue #74 maintainer confirmation, 2026-09-29](https://github.com/ClawBio/ClawBio/issues/74#issuecomment-5885465867) - Network accessline 272
- [Issue #74 maintainer confirmation, 2026-09-29](https://github.com/ClawBio/ClawBio/issues/74#issuecomment-5885465867)
skills/illumina-bridge/illumina_bridge.py
skills/illumina-bridge/illumina_bundle.py
skills/illumina-bridge/illumina_providers.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 18
DEFAULT_ICA_BASE_URL = "https://ica.illumina.com/ica/rest" - Network accessline 18
DEFAULT_ICA_BASE_URL = "https://ica.illumina.com/ica/rest" - Access to secretsline 84
[Credential-related source omitted] - Access to secretsline 84
[Credential-related source omitted] - Access to secretsline 89
[Credential-related source omitted] - Access to secretsline 89
[Credential-related source omitted] - Access to secretsline 90
[Credential-related source omitted] - Access to secretsline 90
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted] - Network accessline 94
self.session = session if self.session is None and requests is not None: self.session = requests.Session() - Network accessline 94
self.session = session if self.session is None and requests is not None: self.session = requests.Session() - Network accessline 95
if self.session is None and requests is not None: self.session = requests.Session() if self.session is not None and hasattr(self.session, "headers"): - Network accessline 95
if self.session is None and requests is not None: self.session = requests.Session() if self.session is not None and hasattr(self.session, "headers"): - Network accessline 96
self.session = requests.Session() - Network accessline 96
self.session = requests.Session() - Access to secretsline 108
[Credential-related source omitted] - Access to secretsline 108
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 147
[Credential-related source omitted] - Access to secretsline 162
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[Credential-related source omitted] - Access to secretsline 261
[Credential-related source omitted] - Access to secretsline 261
[Credential-related source omitted] - Access to secretsline 278
[Credential-related source omitted] - Access to secretsline 278
[Credential-related source omitted]
skills/illumina-bridge/tests/test_illumina_bridge.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted] - Network accessline 72
def raise_for_status(self): response = requests.Response() - Network accessline 72
def raise_for_status(self): response = requests.Response() - Network accessline 73
response = requests.Response() - Network accessline 73
response = requests.Response() - Network accessline 74
response.status_code = self.status_code response.url = "https://tenant.illumina.com/ica/rest/synthetic-private-id" response.raise_for_status() - Network accessline 74
response.status_code = self.status_code response.url = "https://tenant.illumina.com/ica/rest/synthetic-private-id" response.raise_for_status() - Network accessline 75
response.url = "https://tenant.illumina.com/ica/rest/synthetic-private-id" - Network accessline 75
response.url = "https://tenant.illumina.com/ica/rest/synthetic-private-id" - Access to secretsline 254
[Credential-related source omitted] - Access to secretsline 254
[Credential-related source omitted] - Access to secretsline 292
[Credential-related source omitted] - Access to secretsline 292
[Credential-related source omitted] - Network accessline 301
assert result.run["pipeline"] == "DRAGEN Germline 4.3" assert [call["url"] for call in session.calls] == [ f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}", - Network accessline 301
assert result.run["pipeline"] == "DRAGEN Germline 4.3" assert [call["url"] for call in session.calls] == [ f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}", - Network accessline 302
assert [call["url"] for call in session.calls] == [ f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}", f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}/analyses/{ICA_ANALYSIS_ID}", - Network accessline 302
assert [call["url"] for call in session.calls] == [ f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}", f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}/analyses/{ICA_ANALYSIS_ID}", - Network accessline 303
f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}", - Network accessline 303
f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}", - Network accessline 304
f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}/analyses/{ICA_ANALYSIS_ID}", - Network accessline 304
f"https://ica.illumina.com/ica/rest/api/projects/{ICA_PROJECT_ID}/analyses/{ICA_ANALYSIS_ID}", - Access to secretsline 317
[Credential-related source omitted] - Access to secretsline 317
[Credential-related source omitted] - Access to secretsline 329
[Credential-related source omitted] - Access to secretsline 329
[Credential-related source omitted] - Access to secretsline 340
[Credential-related source omitted] - Access to secretsline 340
[Credential-related source omitted] - Access to secretsline 353
[Credential-related source omitted] - Access to secretsline 353
[Credential-related source omitted] - Access to secretsline 363
[Credential-related source omitted] - Access to secretsline 363
[Credential-related source omitted] - Access to secretsline 375
[Credential-related source omitted] - Access to secretsline 375
[Credential-related source omitted] - Access to secretsline 394
[Credential-related source omitted] - Access to secretsline 394
[Credential-related source omitted] - Access to secretsline 395
[Credential-related source omitted] - Access to secretsline 395
[Credential-related source omitted] - Access to secretsline 403
[Credential-related source omitted] - Access to secretsline 403
[Credential-related source omitted] - Access to secretsline 412
[Credential-related source omitted] - Access to secretsline 412
[Credential-related source omitted] - Access to secretsline 424
[Credential-related source omitted] - Access to secretsline 424
[Credential-related source omitted] - Access to secretsline 439
[Credential-related source omitted] - Access to secretsline 439
[Credential-related source omitted] - Network accessline 467
@pytest.mark.parametrize("lookup", ["project", "analysis"]) @pytest.mark.parametrize("error, hint", [ (requests.Timeout("synthetic-private-id"), "timed out"), - Network accessline 467
@pytest.mark.parametrize("lookup", ["project", "analysis"]) @pytest.mark.parametrize("error, hint", [ (requests.Timeout("synthetic-private-id"), "timed out"), - Network accessline 468
@pytest.mark.parametrize("error, hint", [ (requests.Timeout("synthetic-private-id"), "timed out"), (requests.ConnectionError("synthetic-private-id"), "network"), - Network accessline 468
@pytest.mark.parametrize("error, hint", [ (requests.Timeout("synthetic-private-id"), "timed out"), (requests.ConnectionError("synthetic-private-id"), "network"), - Network accessline 469
(requests.Timeout("synthetic-private-id"), "timed out"), - Network accessline 469
(requests.Timeout("synthetic-private-id"), "timed out"), - Network accessline 470
(requests.ConnectionError("synthetic-private-id"), "network"), - Network accessline 470
(requests.ConnectionError("synthetic-private-id"), "network"), - Network accessline 471
(requests.RequestException("synthetic-private-id"), "request failed"), - Network accessline 471
(requests.RequestException("synthetic-private-id"), "request failed"), - Access to secretsline 481
[Credential-related source omitted] - Access to secretsline 481
[Credential-related source omitted] - Access to secretsline 497
[Credential-related source omitted] - Access to secretsline 497
[Credential-related source omitted] - Access to secretsline 506
[Credential-related source omitted] - Access to secretsline 506
[Credential-related source omitted] - Access to secretsline 507
[Credential-related source omitted] - Access to secretsline 507
[Credential-related source omitted] - Access to secretsline 514
[Credential-related source omitted] - Access to secretsline 514
[Credential-related source omitted] - Access to secretsline 520
[Credential-related source omitted] - Access to secretsline 520
[Credential-related source omitted] - Access to secretsline 521
[Credential-related source omitted] - Access to secretsline 521
[Credential-related source omitted] - Access to secretsline 524
[Credential-related source omitted] - Access to secretsline 524
[Credential-related source omitted] - Network accessline 534
[Credential-related source omitted] - Network accessline 534
[Credential-related source omitted] - Network accessline 535
[Credential-related source omitted] - Network accessline 535
[Credential-related source omitted] - Access to secretsline 535
[Credential-related source omitted] - Access to secretsline 535
[Credential-related source omitted] - Network accessline 536
base_url="http://example.com/ica/rest", - Network accessline 536
base_url="http://example.com/ica/rest", - Network accessline 537
session=session, ) assert provider.base_url == "https://ica.illumina.com/ica/rest" - Network accessline 537
session=session, ) assert provider.base_url == "https://ica.illumina.com/ica/rest" - Network accessline 538
) assert provider.base_url == "https://ica.illumina.com/ica/rest" result = provider.enrich( - Network accessline 538
) assert provider.base_url == "https://ica.illumina.com/ica/rest" result = provider.enrich( - Network accessline 539
assert provider.base_url == "https://ica.illumina.com/ica/rest" - Network accessline 539
assert provider.base_url == "https://ica.illumina.com/ica/rest" - Network accessline 551
[Credential-related source omitted] - Network accessline 551
[Credential-related source omitted] - Network accessline 552
[Credential-related source omitted] - Network accessline 552
[Credential-related source omitted] - Access to secretsline 552
[Credential-related source omitted] - Access to secretsline 552
[Credential-related source omitted] - Network accessline 553
base_url="https://tenant.illumina.com/ica/rest", - Network accessline 553
base_url="https://tenant.illumina.com/ica/rest", - Network accessline 554
session=session, ) assert provider.base_url == "https://tenant.illumina.com/ica/rest" - Network accessline 554
session=session, ) assert provider.base_url == "https://tenant.illumina.com/ica/rest" - Network accessline 555
) assert provider.base_url == "https://tenant.illumina.com/ica/rest" assert provider._initialization_warnings == [] - Network accessline 555
) assert provider.base_url == "https://tenant.illumina.com/ica/rest" assert provider._initialization_warnings == [] - Network accessline 556
assert provider.base_url == "https://tenant.illumina.com/ica/rest" - Network accessline 556
assert provider.base_url == "https://tenant.illumina.com/ica/rest" - Access to secretsline 566
[Credential-related source omitted] - Access to secretsline 566
[Credential-related source omitted] - Access to secretsline 680
[Credential-related source omitted] - Access to secretsline 680
[Credential-related source omitted]
skills/just-prs-mcp/SKILL.md
- Network accessline 54
always: false emoji: "🧬" homepage: https://github.com/dna-seq/just-prs-mcp - Network accessline 54
always: false emoji: "🧬" homepage: https://github.com/dna-seq/just-prs-mcp - Network accessline 55
emoji: "🧬" homepage: https://github.com/dna-seq/just-prs-mcp os: - Network accessline 55
emoji: "🧬" homepage: https://github.com/dna-seq/just-prs-mcp os: - Network accessline 56
homepage: https://github.com/dna-seq/just-prs-mcp - Network accessline 56
homepage: https://github.com/dna-seq/just-prs-mcp - Network accessline 328
- [PGS Catalog](https://www.pgscatalog.org/); public score metadata and scoring files. - Network accessline 328
- [PGS Catalog](https://www.pgscatalog.org/); public score metadata and scoring files. - Network accessline 329
- [just-prs](https://github.com/dna-seq/just-prs); scoring, normalization, - Network accessline 329
- [just-prs](https://github.com/dna-seq/just-prs); scoring, normalization, - Network accessline 330
percentile, quality, and PLINK2 parity validation. - [just-prs-mcp](https://github.com/dna-seq/just-prs-mcp); typed MCP contracts, curated trait workflow, and local stdio privacy boundary. - Network accessline 330
percentile, quality, and PLINK2 parity validation. - [just-prs-mcp](https://github.com/dna-seq/just-prs-mcp); typed MCP contracts, curated trait workflow, and local stdio privacy boundary. - Network accessline 331
- [just-prs-mcp](https://github.com/dna-seq/just-prs-mcp); typed MCP contracts, - Network accessline 331
- [just-prs-mcp](https://github.com/dna-seq/just-prs-mcp); typed MCP contracts, - Network accessline 332
curated trait workflow, and local stdio privacy boundary. - [just-dna-lite FAQ](https://github.com/dna-seq/just-dna-lite/blob/main/docs/FAQ.md); local computation, user ownership, open access, and citizen-science context. - Network accessline 332
curated trait workflow, and local stdio privacy boundary. - [just-dna-lite FAQ](https://github.com/dna-seq/just-dna-lite/blob/main/docs/FAQ.md); local computation, user ownership, open access, and citizen-science context. - Network accessline 333
- [just-dna-lite FAQ](https://github.com/dna-seq/just-dna-lite/blob/main/docs/FAQ.md); - Network accessline 333
- [just-dna-lite FAQ](https://github.com/dna-seq/just-dna-lite/blob/main/docs/FAQ.md);
skills/just-prs-mcp/just_prs_mcp_bridge.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 133
[Credential-related source omitted] - Access to secretsline 133
[Credential-related source omitted] - Network accessline 241
"pgs_id": pgs_id, "pgs_catalog_url": ( f"https://www.pgscatalog.org/score/{pgs_id}/" if pgs_id else None - Network accessline 241
"pgs_id": pgs_id, "pgs_catalog_url": ( f"https://www.pgscatalog.org/score/{pgs_id}/" if pgs_id else None - Network accessline 242
"pgs_catalog_url": ( f"https://www.pgscatalog.org/score/{pgs_id}/" if pgs_id else None ), - Network accessline 242
"pgs_catalog_url": ( f"https://www.pgscatalog.org/score/{pgs_id}/" if pgs_id else None ), - Network accessline 243
f"https://www.pgscatalog.org/score/{pgs_id}/" if pgs_id else None - Network accessline 243
f"https://www.pgscatalog.org/score/{pgs_id}/" if pgs_id else None
skills/just-prs-mcp/mcp_client.py
skills/just-prs-mcp/tests/test_just_prs_mcp.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 89
[Credential-related source omitted] - Access to secretsline 89
[Credential-related source omitted] - Access to secretsline 448
[Credential-related source omitted] - Access to secretsline 448
[Credential-related source omitted] - Access to secretsline 598
[Credential-related source omitted] - Access to secretsline 598
[Credential-related source omitted]
skills/just-prs-mcp/tests/test_live_integration.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 77
[Credential-related source omitted] - Access to secretsline 77
[Credential-related source omitted]
skills/labstep/SKILL.md
- Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Network accessline 23
always: false emoji: 🔬 homepage: https://www.labstep.com - Network accessline 23
always: false emoji: 🔬 homepage: https://www.labstep.com - Network accessline 24
emoji: 🔬 homepage: https://www.labstep.com os: - Network accessline 24
emoji: 🔬 homepage: https://www.labstep.com os: - Network accessline 25
homepage: https://www.labstep.com - Network accessline 25
homepage: https://www.labstep.com - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 55
[Credential-related source omitted] - Access to secretsline 60
[Credential-related source omitted] - Access to secretsline 60
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 76
[Credential-related source omitted] - Access to secretsline 261
[Credential-related source omitted] - Access to secretsline 261
[Credential-related source omitted]
skills/labstep/labstep.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 65
[Credential-related source omitted] - Access to secretsline 65
[Credential-related source omitted] - Access to secretsline 69
[Credential-related source omitted] - Access to secretsline 69
[Credential-related source omitted]
skills/labstep/tests/test_labstep.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 368
[Credential-related source omitted] - Access to secretsline 368
[Credential-related source omitted] - Access to secretsline 374
[Credential-related source omitted] - Access to secretsline 374
[Credential-related source omitted]
skills/ld-1000g-region-compute/SKILL.md
- Network accessline 55
- examples/input.json endpoints: - https://ftp.1000genomes.ebi.ac.uk/ # phased VCFs + panel TSV (on-demand mode) - Network accessline 55
- examples/input.json endpoints: - https://ftp.1000genomes.ebi.ac.uk/ # phased VCFs + panel TSV (on-demand mode) - Network accessline 56
endpoints: - https://ftp.1000genomes.ebi.ac.uk/ # phased VCFs + panel TSV (on-demand mode) openclaw: - Network accessline 56
endpoints: - https://ftp.1000genomes.ebi.ac.uk/ # phased VCFs + panel TSV (on-demand mode) openclaw: - Network accessline 57
- https://ftp.1000genomes.ebi.ac.uk/ # phased VCFs + panel TSV (on-demand mode) - Network accessline 57
- https://ftp.1000genomes.ebi.ac.uk/ # phased VCFs + panel TSV (on-demand mode) - Network accessline 66
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 66
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 67
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 67
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 68
homepage: https://github.com/ClawBio/ClawBio - Network accessline 68
homepage: https://github.com/ClawBio/ClawBio - Network accessline 76
# Ubuntu / Debian: apt-get install plink1.9 # any platform: conda install -c bioconda plink # direct binary: https://www.cog-genomics.org/plink/1.9/ (then set PLINK_BIN) - Network accessline 76
# Ubuntu / Debian: apt-get install plink1.9 # any platform: conda install -c bioconda plink # direct binary: https://www.cog-genomics.org/plink/1.9/ (then set PLINK_BIN) - Network accessline 77
# any platform: conda install -c bioconda plink # direct binary: https://www.cog-genomics.org/plink/1.9/ (then set PLINK_BIN) trigger_keywords: - Network accessline 77
# any platform: conda install -c bioconda plink # direct binary: https://www.cog-genomics.org/plink/1.9/ (then set PLINK_BIN) trigger_keywords: - Network accessline 78
# direct binary: https://www.cog-genomics.org/plink/1.9/ (then set PLINK_BIN) - Network accessline 78
# direct binary: https://www.cog-genomics.org/plink/1.9/ (then set PLINK_BIN) - Network accessline 127
1. **Resolve `lead` + `partners` + `chromosome` + `window_bp` + `super_pop`**: lead in `chr_pos_ref_alt` GRCh38 form; partners as a list (or `null` to compute against all variants in the window); super-population from `{EUR, AFR, AMR, EAS, - Network accessline 127
1. **Resolve `lead` + `partners` + `chromosome` + `window_bp` + `super_pop`**: lead in `chr_pos_ref_alt` GRCh38 form; partners as a list (or `null` to compute against all variants in the window); super-population from `{EUR, AFR, AMR, EAS, - Network accessline 128
2. **Region VCF fetch**: the skill performs a tabix-on-FTP byte-range request against `https://ftp.1000genomes.ebi.ac.uk/` for the requested chromosome × window. Cache hit at `~/.clawbio/locuscompare_cache/1000g/<chr>_<start>_<end>.vcf.gz` - Network accessline 128
2. **Region VCF fetch**: the skill performs a tabix-on-FTP byte-range request against `https://ftp.1000genomes.ebi.ac.uk/` for the requested chromosome × window. Cache hit at `~/.clawbio/locuscompare_cache/1000g/<chr>_<start>_<end>.vcf.gz` - Network accessline 237
4. **plink 1.9 `--keep` FID convention.** plink 1.9 + `--vcf` assigns `FID = IID = sample-id` (per [the plink 1.9 input docs](https://www.cog-genomics.org/plink/1.9/data#vcf)); the on-demand client's `--keep` file therefore writes `<sample> - Network accessline 237
4. **plink 1.9 `--keep` FID convention.** plink 1.9 + `--vcf` assigns `FID = IID = sample-id` (per [the plink 1.9 input docs](https://www.cog-genomics.org/plink/1.9/data#vcf)); the on-demand client's `--keep` file therefore writes `<sample>
skills/ld-1000g-region-compute/examples/run_example.sh
skills/ld-1000g-region-compute/ld_1000g_region_compute.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 16
Nature, Clarke 2017 NAR). Treated as Green-with-attribution. - plink 1.9 binary: GPL-3 standalone. Subprocess invocation is FSF mere aggregation (https://www.gnu.org/licenses/gpl-faq.html#MereAggregation), - Network accessline 16
Nature, Clarke 2017 NAR). Treated as Green-with-attribution. - plink 1.9 binary: GPL-3 standalone. Subprocess invocation is FSF mere aggregation (https://www.gnu.org/licenses/gpl-faq.html#MereAggregation), - Network accessline 17
- plink 1.9 binary: GPL-3 standalone. Subprocess invocation is FSF mere aggregation (https://www.gnu.org/licenses/gpl-faq.html#MereAggregation), not linkage. Codebase remains MIT. Do NOT bundle the binary in our - Network accessline 17
- plink 1.9 binary: GPL-3 standalone. Subprocess invocation is FSF mere aggregation (https://www.gnu.org/licenses/gpl-faq.html#MereAggregation), not linkage. Codebase remains MIT. Do NOT bundle the binary in our - Network accessline 18
aggregation (https://www.gnu.org/licenses/gpl-faq.html#MereAggregation), - Network accessline 18
aggregation (https://www.gnu.org/licenses/gpl-faq.html#MereAggregation), - Access to secretsline 107
[Credential-related source omitted] - Access to secretsline 107
[Credential-related source omitted]
skills/ld-1000g-region-compute/ondemand_client.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 37
ONEKG_VCF_URL_TEMPLATE = ( "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/" - Network accessline 37
ONEKG_VCF_URL_TEMPLATE = ( "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/" - Network accessline 38
"https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/" - Network accessline 38
"https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/" - Network accessline 41
) ONEKG_PANEL_URL = ( "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" - Network accessline 41
) ONEKG_PANEL_URL = ( "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" - Network accessline 42
ONEKG_PANEL_URL = ( "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" "integrated_call_samples_v3.20130502.ALL.panel" - Network accessline 42
ONEKG_PANEL_URL = ( "https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" "integrated_call_samples_v3.20130502.ALL.panel" - Network accessline 43
"https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" - Network accessline 43
"https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 56
[Credential-related source omitted] - Network accessline 60
"(macOS), `apt-get install plink1.9` (Ubuntu/Debian), or " "`conda install -c bioconda plink` (any platform); direct binary " "downloads are available at https://www.cog-genomics.org/plink/1.9/. " - Network accessline 60
"(macOS), `apt-get install plink1.9` (Ubuntu/Debian), or " "`conda install -c bioconda plink` (any platform); direct binary " "downloads are available at https://www.cog-genomics.org/plink/1.9/. " - Network accessline 61
"`conda install -c bioconda plink` (any platform); direct binary " "downloads are available at https://www.cog-genomics.org/plink/1.9/. " "Then either ensure it is on PATH or set PLINK_BIN to its absolute path." - Network accessline 61
"`conda install -c bioconda plink` (any platform); direct binary " "downloads are available at https://www.cog-genomics.org/plink/1.9/. " "Then either ensure it is on PATH or set PLINK_BIN to its absolute path." - Network accessline 62
"downloads are available at https://www.cog-genomics.org/plink/1.9/. " - Network accessline 62
"downloads are available at https://www.cog-genomics.org/plink/1.9/. " - Network accessline 113
"""Fetch (or read from cache) the 1000G sample to super_pop mapping; - Network accessline 113
"""Fetch (or read from cache) the 1000G sample to super_pop mapping; - Network accessline 117
if not panel_path.is_file(): cache_dir.mkdir(parents=True, exist_ok=True) resp = requests.get(ONEKG_PANEL_URL, timeout=60) - Network accessline 117
if not panel_path.is_file(): cache_dir.mkdir(parents=True, exist_ok=True) resp = requests.get(ONEKG_PANEL_URL, timeout=60) - Network accessline 118
cache_dir.mkdir(parents=True, exist_ok=True) resp = requests.get(ONEKG_PANEL_URL, timeout=60) resp.raise_for_status() - Network accessline 118
cache_dir.mkdir(parents=True, exist_ok=True) resp = requests.get(ONEKG_PANEL_URL, timeout=60) resp.raise_for_status() - Network accessline 119
resp = requests.get(ONEKG_PANEL_URL, timeout=60) - Network accessline 119
resp = requests.get(ONEKG_PANEL_URL, timeout=60) - Network accessline 159
with tmp_vcf.open("w") as out: out.write(str(src.header)) for rec in src.fetch(chrom_used, start_bp, end_bp): - Network accessline 159
with tmp_vcf.open("w") as out: out.write(str(src.header)) for rec in src.fetch(chrom_used, start_bp, end_bp): - Network accessline 160
out.write(str(src.header)) for rec in src.fetch(chrom_used, start_bp, end_bp): out.write(str(rec)) - Network accessline 160
out.write(str(src.header)) for rec in src.fetch(chrom_used, start_bp, end_bp): out.write(str(rec)) - Network accessline 161
for rec in src.fetch(chrom_used, start_bp, end_bp): - Network accessline 161
for rec in src.fetch(chrom_used, start_bp, end_bp): - Network accessline 249
# plink 1.9 `--vcf` assigns FID=IID=sample-id (per # https://www.cog-genomics.org/plink/1.9/data#vcf). `--keep` - Network accessline 249
# plink 1.9 `--vcf` assigns FID=IID=sample-id (per # https://www.cog-genomics.org/plink/1.9/data#vcf). `--keep` - Network accessline 250
# https://www.cog-genomics.org/plink/1.9/data#vcf). `--keep` - Network accessline 250
# https://www.cog-genomics.org/plink/1.9/data#vcf). `--keep`
skills/ld-1000g-region-compute/tests/conftest.py
skills/ld-1000g-region-compute/tests/test_ld_1000g_region_compute.py
skills/ld-1000g-region-compute/tests/test_live_ld_1000g_region_compute.py
skills/lit-synthesizer/SKILL.md
- Network accessline 38
requires: always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 38
requires: always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 39
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 39
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 40
homepage: https://github.com/ClawBio/ClawBio - Network accessline 40
homepage: https://github.com/ClawBio/ClawBio - Network accessline 172
2. **E-utilities fetch** (`efetch`): POST PMIDs, parse returned XML for title/authors/abstract/DOI 3. **Rate limiting**: 0.34 s sleep between NCBI requests (respects 3 req/s limit) 4. **bioRxiv API**: GET `https://api.biorxiv.org/details/bi - Network accessline 172
2. **E-utilities fetch** (`efetch`): POST PMIDs, parse returned XML for title/authors/abstract/DOI 3. **Rate limiting**: 0.34 s sleep between NCBI requests (respects 3 req/s limit) 4. **bioRxiv API**: GET `https://api.biorxiv.org/details/bi - Network accessline 173
3. **Rate limiting**: 0.34 s sleep between NCBI requests (respects 3 req/s limit) 4. **bioRxiv API**: GET `https://api.biorxiv.org/details/biorxiv/{date_range}/0/json`, filter by keywords 5. **Citation graph**: Build node per paper (PMID or - Network accessline 173
3. **Rate limiting**: 0.34 s sleep between NCBI requests (respects 3 req/s limit) 4. **bioRxiv API**: GET `https://api.biorxiv.org/details/biorxiv/{date_range}/0/json`, filter by keywords 5. **Citation graph**: Build node per paper (PMID or - Network accessline 174
4. **bioRxiv API**: GET `https://api.biorxiv.org/details/biorxiv/{date_range}/0/json`, filter by keywords - Network accessline 174
4. **bioRxiv API**: GET `https://api.biorxiv.org/details/biorxiv/{date_range}/0/json`, filter by keywords - Network accessline 303
- [NCBI E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25499/); PubMed programmatic search API - Network accessline 303
- [NCBI E-utilities](https://www.ncbi.nlm.nih.gov/books/NBK25499/); PubMed programmatic search API - Network accessline 304
- [bioRxiv API](https://api.biorxiv.org/); preprint search and metadata - Network accessline 304
- [bioRxiv API](https://api.biorxiv.org/); preprint search and metadata - Network accessline 305
- [Biopython Entrez module](https://biopython.org/docs/latest/api/Bio.Entrez.html); Python wrapper for E-utilities - Network accessline 305
- [Biopython Entrez module](https://biopython.org/docs/latest/api/Bio.Entrez.html); Python wrapper for E-utilities
skills/lit-synthesizer/examples/demo_output/report.md
- Network accessline 25
| **Year** | 2016 | | **DOI** | 10.1038/nature17946 | | **URL** | [https://pubmed.ncbi.nlm.nih.gov/27096365](https://pubmed.ncbi.nlm.nih.gov/27096365) | - Network accessline 25
| **Year** | 2016 | | **DOI** | 10.1038/nature17946 | | **URL** | [https://pubmed.ncbi.nlm.nih.gov/27096365](https://pubmed.ncbi.nlm.nih.gov/27096365) | - Network accessline 27
| **URL** | [https://pubmed.ncbi.nlm.nih.gov/27096365](https://pubmed.ncbi.nlm.nih.gov/27096365) | - Network accessline 27
| **URL** | [https://pubmed.ncbi.nlm.nih.gov/27096365](https://pubmed.ncbi.nlm.nih.gov/27096365) | - Network accessline 38
| **Year** | 2017 | | **DOI** | 10.1038/nature24644 | | **URL** | [https://pubmed.ncbi.nlm.nih.gov/29160308](https://pubmed.ncbi.nlm.nih.gov/29160308) | - Network accessline 38
| **Year** | 2017 | | **DOI** | 10.1038/nature24644 | | **URL** | [https://pubmed.ncbi.nlm.nih.gov/29160308](https://pubmed.ncbi.nlm.nih.gov/29160308) | - Network accessline 40
| **URL** | [https://pubmed.ncbi.nlm.nih.gov/29160308](https://pubmed.ncbi.nlm.nih.gov/29160308) | - Network accessline 40
| **URL** | [https://pubmed.ncbi.nlm.nih.gov/29160308](https://pubmed.ncbi.nlm.nih.gov/29160308) | - Network accessline 51
| **Year** | 2019 | | **DOI** | 10.1038/s41586-019-1711-4 | | **URL** | [https://pubmed.ncbi.nlm.nih.gov/31634902](https://pubmed.ncbi.nlm.nih.gov/31634902) | - Network accessline 51
| **Year** | 2019 | | **DOI** | 10.1038/s41586-019-1711-4 | | **URL** | [https://pubmed.ncbi.nlm.nih.gov/31634902](https://pubmed.ncbi.nlm.nih.gov/31634902) | - Network accessline 53
| **URL** | [https://pubmed.ncbi.nlm.nih.gov/31634902](https://pubmed.ncbi.nlm.nih.gov/31634902) | - Network accessline 53
| **URL** | [https://pubmed.ncbi.nlm.nih.gov/31634902](https://pubmed.ncbi.nlm.nih.gov/31634902) | - Network accessline 64
| **Year** | 2026 | | **DOI** | 10.64898/2026.07.06.736660 | | **URL** | [https://biorxiv.org/content/10.64898/2026.07.06.736660](https://biorxiv.org/content/10.64898/2026.07.06.736660) | - Network accessline 64
| **Year** | 2026 | | **DOI** | 10.64898/2026.07.06.736660 | | **URL** | [https://biorxiv.org/content/10.64898/2026.07.06.736660](https://biorxiv.org/content/10.64898/2026.07.06.736660) | - Network accessline 66
| **URL** | [https://biorxiv.org/content/10.64898/2026.07.06.736660](https://biorxiv.org/content/10.64898/2026.07.06.736660) | - Network accessline 66
| **URL** | [https://biorxiv.org/content/10.64898/2026.07.06.736660](https://biorxiv.org/content/10.64898/2026.07.06.736660) |
skills/lit-synthesizer/examples/demo_papers.json
- Network accessline 15
"abstract": "Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. Although most genetic diseases arise from point mutations, current approaches to point mutati - Network accessline 15
"abstract": "Current genome-editing technologies introduce double-stranded (ds) DNA breaks at a target locus as the first step to gene correction. Although most genetic diseases arise from point mutations, current approaches to point mutati - Network accessline 16
"doi": "10.1038/nature17946", "url": "https://pubmed.ncbi.nlm.nih.gov/27096365", "citations": [] - Network accessline 16
"doi": "10.1038/nature17946", "url": "https://pubmed.ncbi.nlm.nih.gov/27096365", "citations": [] - Network accessline 17
"url": "https://pubmed.ncbi.nlm.nih.gov/27096365", - Network accessline 17
"url": "https://pubmed.ncbi.nlm.nih.gov/27096365", - Network accessline 35
"abstract": "The spontaneous deamination of cytosine is a major source of transitions from C•G to T•A base pairs, which account for half of known pathogenic point mutations in humans. The ability to efficiently convert targeted A•T base pai - Network accessline 35
"abstract": "The spontaneous deamination of cytosine is a major source of transitions from C•G to T•A base pairs, which account for half of known pathogenic point mutations in humans. The ability to efficiently convert targeted A•T base pai - Network accessline 36
"doi": "10.1038/nature24644", "url": "https://pubmed.ncbi.nlm.nih.gov/29160308", "citations": [ - Network accessline 36
"doi": "10.1038/nature24644", "url": "https://pubmed.ncbi.nlm.nih.gov/29160308", "citations": [ - Network accessline 37
"url": "https://pubmed.ncbi.nlm.nih.gov/29160308", - Network accessline 37
"url": "https://pubmed.ncbi.nlm.nih.gov/29160308", - Network accessline 61
"abstract": "Most genetic variants that contribute to disease1 are challenging to correct efficiently and without excess byproducts2-5. Here we describe prime editing, a versatile and precise genome editing method that directly writes new g - Network accessline 61
"abstract": "Most genetic variants that contribute to disease1 are challenging to correct efficiently and without excess byproducts2-5. Here we describe prime editing, a versatile and precise genome editing method that directly writes new g - Network accessline 62
"doi": "10.1038/s41586-019-1711-4", "url": "https://pubmed.ncbi.nlm.nih.gov/31634902", "citations": [ - Network accessline 62
"doi": "10.1038/s41586-019-1711-4", "url": "https://pubmed.ncbi.nlm.nih.gov/31634902", "citations": [ - Network accessline 63
"url": "https://pubmed.ncbi.nlm.nih.gov/31634902", - Network accessline 63
"url": "https://pubmed.ncbi.nlm.nih.gov/31634902", - Network accessline 84
"abstract": "Prime editing enables the precise modification of genomes, thereby holding great potential for the treatment of genetic diseases. Despite substantial advancements in prime editing technology and the initiation of the first clin - Network accessline 84
"abstract": "Prime editing enables the precise modification of genomes, thereby holding great potential for the treatment of genetic diseases. Despite substantial advancements in prime editing technology and the initiation of the first clin - Network accessline 85
"doi": "10.64898/2026.07.06.736660", "url": "https://biorxiv.org/content/10.64898/2026.07.06.736660", "citations": [] - Network accessline 85
"doi": "10.64898/2026.07.06.736660", "url": "https://biorxiv.org/content/10.64898/2026.07.06.736660", "citations": [] - Network accessline 86
"url": "https://biorxiv.org/content/10.64898/2026.07.06.736660", - Network accessline 86
"url": "https://biorxiv.org/content/10.64898/2026.07.06.736660",
skills/lit-synthesizer/examples/demo_sources/biorxiv_details.json
- Network accessline 18
"license": "cc_by_nc", "category": "molecular biology", "jatsxml": "https://www.biorxiv.org/content/early/2026/07/07/2026.07.06.736660.source.xml", - Network accessline 18
"license": "cc_by_nc", "category": "molecular biology", "jatsxml": "https://www.biorxiv.org/content/early/2026/07/07/2026.07.06.736660.source.xml", - Network accessline 19
"category": "molecular biology", "jatsxml": "https://www.biorxiv.org/content/early/2026/07/07/2026.07.06.736660.source.xml", "abstract": "Prime editing enables the precise modification of genomes, thereby holding great potential for t - Network accessline 19
"category": "molecular biology", "jatsxml": "https://www.biorxiv.org/content/early/2026/07/07/2026.07.06.736660.source.xml", "abstract": "Prime editing enables the precise modification of genomes, thereby holding great potential for t - Network accessline 20
"jatsxml": "https://www.biorxiv.org/content/early/2026/07/07/2026.07.06.736660.source.xml", - Network accessline 20
"jatsxml": "https://www.biorxiv.org/content/early/2026/07/07/2026.07.06.736660.source.xml",
skills/lit-synthesizer/examples/demo_sources/fetch_demo_sources.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 20
PMIDS = ["27096365", "29160308", "31634902"] BIORXIV_DOI = "10.64898/2026.07.06.736660" EUTILS = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Network accessline 20
PMIDS = ["27096365", "29160308", "31634902"] BIORXIV_DOI = "10.64898/2026.07.06.736660" EUTILS = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Network accessline 22
EUTILS = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Network accessline 22
EUTILS = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils" - Network accessline 25
def _get(url: str) -> bytes: with urllib.request.urlopen(url, timeout=30) as resp: - Network accessline 25
def _get(url: str) -> bytes: with urllib.request.urlopen(url, timeout=30) as resp: - Network accessline 26
with urllib.request.urlopen(url, timeout=30) as resp: - Network accessline 26
with urllib.request.urlopen(url, timeout=30) as resp: - Network accessline 30
def fetch() -> None: - Network accessline 30
def fetch() -> None: - Network accessline 41
refs = json.loads(_get(elink)) (HERE / "pubmed_elink_refs.json").write_text(json.dumps(refs, indent=1) + "\n") details = json.loads(_get(f"https://api.biorxiv.org/details/biorxiv/{BIORXIV_DOI}")) - Network accessline 41
refs = json.loads(_get(elink)) (HERE / "pubmed_elink_refs.json").write_text(json.dumps(refs, indent=1) + "\n") details = json.loads(_get(f"https://api.biorxiv.org/details/biorxiv/{BIORXIV_DOI}")) - Network accessline 42
(HERE / "pubmed_elink_refs.json").write_text(json.dumps(refs, indent=1) + "\n") details = json.loads(_get(f"https://api.biorxiv.org/details/biorxiv/{BIORXIV_DOI}")) (HERE / "biorxiv_details.json").write_text(json.dumps(details, inde - Network accessline 42
(HERE / "pubmed_elink_refs.json").write_text(json.dumps(refs, indent=1) + "\n") details = json.loads(_get(f"https://api.biorxiv.org/details/biorxiv/{BIORXIV_DOI}")) (HERE / "biorxiv_details.json").write_text(json.dumps(details, inde - Network accessline 43
details = json.loads(_get(f"https://api.biorxiv.org/details/biorxiv/{BIORXIV_DOI}")) - Network accessline 43
details = json.loads(_get(f"https://api.biorxiv.org/details/biorxiv/{BIORXIV_DOI}")) - Network accessline 66
if __name__ == "__main__": if "--offline" not in sys.argv[1:]: fetch() - Network accessline 66
if __name__ == "__main__": if "--offline" not in sys.argv[1:]: fetch() - Network accessline 67
if "--offline" not in sys.argv[1:]: fetch() build() - Network accessline 67
if "--offline" not in sys.argv[1:]: fetch() build() - Network accessline 68
fetch() - Network accessline 68
fetch()
skills/lit-synthesizer/examples/demo_sources/pubmed_efetch.xml
- Network accessline 1
<?xml version="1.0" ?> <!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd"> - Network accessline 1
<?xml version="1.0" ?> <!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd"> - Network accessline 2
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd"> - Network accessline 2
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2025//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_250101.dtd">
skills/lit-synthesizer/lit_synthesizer.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 28
PUBMED_SEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 28
PUBMED_SEARCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 29
PUBMED_FETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" - Network accessline 29
PUBMED_FETCH_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" - Network accessline 30
BIORXIV_API_URL = "https://api.biorxiv.org/details/biorxiv" - Network accessline 30
BIORXIV_API_URL = "https://api.biorxiv.org/details/biorxiv" - Network accessline 64
url = f"{PUBMED_SEARCH_URL}?{params}" try: with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 64
url = f"{PUBMED_SEARCH_URL}?{params}" try: with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 65
try: with urllib.request.urlopen(url, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 65
try: with urllib.request.urlopen(url, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 66
with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 66
with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 86
url = f"{PUBMED_FETCH_URL}?{params}" try: with urllib.request.urlopen(url, timeout=15) as resp: - Network accessline 86
url = f"{PUBMED_FETCH_URL}?{params}" try: with urllib.request.urlopen(url, timeout=15) as resp: - Network accessline 87
try: with urllib.request.urlopen(url, timeout=15) as resp: xml_data = resp.read() - Network accessline 87
try: with urllib.request.urlopen(url, timeout=15) as resp: xml_data = resp.read() - Network accessline 88
with urllib.request.urlopen(url, timeout=15) as resp: - Network accessline 88
with urllib.request.urlopen(url, timeout=15) as resp: - Network accessline 133
"abstract": " ".join(p for p in abstract_parts if p) or "No abstract available.", "doi": doi_el.text if doi_el is not None else "", "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}", - Network accessline 133
"abstract": " ".join(p for p in abstract_parts if p) or "No abstract available.", "doi": doi_el.text if doi_el is not None else "", "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}", - Network accessline 134
"doi": doi_el.text if doi_el is not None else "", "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}", "citations": [], - Network accessline 134
"doi": doi_el.text if doi_el is not None else "", "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}", "citations": [], - Network accessline 135
"url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}", - Network accessline 135
"url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}", - Network accessline 152
"abstract": item.get("abstract", "No abstract available."), "doi": item.get("doi", ""), "url": f"https://biorxiv.org/content/{item.get('doi', '')}", - Network accessline 152
"abstract": item.get("abstract", "No abstract available."), "doi": item.get("doi", ""), "url": f"https://biorxiv.org/content/{item.get('doi', '')}", - Network accessline 153
"doi": item.get("doi", ""), "url": f"https://biorxiv.org/content/{item.get('doi', '')}", "citations": [], - Network accessline 153
"doi": item.get("doi", ""), "url": f"https://biorxiv.org/content/{item.get('doi', '')}", "citations": [], - Network accessline 154
"url": f"https://biorxiv.org/content/{item.get('doi', '')}", - Network accessline 154
"url": f"https://biorxiv.org/content/{item.get('doi', '')}", - Network accessline 167
papers = [] try: with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 167
papers = [] try: with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 168
try: with urllib.request.urlopen(url, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 168
try: with urllib.request.urlopen(url, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 169
with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 169
with urllib.request.urlopen(url, timeout=10) as resp:
skills/lit-synthesizer/tests/test_demo_provenance.py
skills/lit-synthesizer/tests/test_lit_synthesizer.py
skills/locuscompare-region-render/INPUT_SCHEMA.md
- Network accessline 105
"molecular_trait_id": "ENSG00000134243", "fetched_at": "2026-05-06T14:32:17Z", "fetched_via": "tabix-on-FTP at https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/...", - Network accessline 105
"molecular_trait_id": "ENSG00000134243", "fetched_at": "2026-05-06T14:32:17Z", "fetched_via": "tabix-on-FTP at https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/...", - Network accessline 106
"fetched_at": "2026-05-06T14:32:17Z", "fetched_via": "tabix-on-FTP at https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/...", "region": {"chromosome": "1", "start_bp": 108774968, "end_bp": 109774968}, - Network accessline 106
"fetched_at": "2026-05-06T14:32:17Z", "fetched_via": "tabix-on-FTP at https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/...", "region": {"chromosome": "1", "start_bp": 108774968, "end_bp": 109774968}, - Network accessline 107
"fetched_via": "tabix-on-FTP at https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/...", - Network accessline 107
"fetched_via": "tabix-on-FTP at https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/...", - Network accessline 113
"harmonisation_version": "", "effect_allele_convention": "allele_b is effect allele", "source_native_format_link": "https://www.ebi.ac.uk/eqtl/Studies/" - Network accessline 113
"harmonisation_version": "", "effect_allele_convention": "allele_b is effect allele", "source_native_format_link": "https://www.ebi.ac.uk/eqtl/Studies/" - Network accessline 114
"effect_allele_convention": "allele_b is effect allele", "source_native_format_link": "https://www.ebi.ac.uk/eqtl/Studies/" } - Network accessline 114
"effect_allele_convention": "allele_b is effect allele", "source_native_format_link": "https://www.ebi.ac.uk/eqtl/Studies/" } - Network accessline 115
"source_native_format_link": "https://www.ebi.ac.uk/eqtl/Studies/" - Network accessline 115
"source_native_format_link": "https://www.ebi.ac.uk/eqtl/Studies/"
skills/locuscompare-region-render/SKILL.md
- Network accessline 57
- examples/02_eqtl_catalogue_x_gwas_catalog/config.yaml endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # eQTL Catalogue tabix-on-FTP - Network accessline 57
- examples/02_eqtl_catalogue_x_gwas_catalog/config.yaml endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # eQTL Catalogue tabix-on-FTP - Network accessline 58
endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # eQTL Catalogue tabix-on-FTP - https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # GWAS Catalog harmonised tabix-on-FTP - Network accessline 58
endpoints: - https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # eQTL Catalogue tabix-on-FTP - https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # GWAS Catalog harmonised tabix-on-FTP - Network accessline 59
- https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # eQTL Catalogue tabix-on-FTP - Network accessline 59
- https://ftp.ebi.ac.uk/pub/databases/spot/eQTL/sumstats/ # eQTL Catalogue tabix-on-FTP - Network accessline 60
- https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # GWAS Catalog harmonised tabix-on-FTP - Network accessline 60
- https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/ # GWAS Catalog harmonised tabix-on-FTP - Network accessline 61
- https://ftp.1000genomes.ebi.ac.uk/ # 1000G phased VCFs (LD compute) - Network accessline 61
- https://ftp.1000genomes.ebi.ac.uk/ # 1000G phased VCFs (LD compute) - Network accessline 62
- https://rest.ensembl.org/ # GENCODE gene-track REST - Network accessline 62
- https://rest.ensembl.org/ # GENCODE gene-track REST - Network accessline 71
always: false emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio - Network accessline 71
always: false emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio - Network accessline 72
emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 72
emoji: "🎯" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 73
homepage: https://github.com/ClawBio/ClawBio - Network accessline 73
homepage: https://github.com/ClawBio/ClawBio - Network accessline 137
1. **Validate**: parse the config (JSON or YAML); validate against the embedded pydantic schema; check input files exist and conform to `INPUT_SCHEMA.md`. The lead variant must be in `chr_pos_ref_alt` GRCh38 form; the window defaults to ±50 - Network accessline 137
1. **Validate**: parse the config (JSON or YAML); validate against the embedded pydantic schema; check input files exist and conform to `INPUT_SCHEMA.md`. The lead variant must be in `chr_pos_ref_alt` GRCh38 form; the window defaults to ±50 - Network accessline 138
2. **Fetch (optional)**: for each side using a bundled fetcher (`source: eqtl_catalogue` or `source: gwas_catalog`), tabix-fetch the region from the source's FTP via the corresponding sibling skill (`eqtl-catalogue-region-fetch` or `gwas-ca - Network accessline 138
2. **Fetch (optional)**: for each side using a bundled fetcher (`source: eqtl_catalogue` or `source: gwas_catalog`), tabix-fetch the region from the source's FTP via the corresponding sibling skill (`eqtl-catalogue-region-fetch` or `gwas-ca
skills/locuscompare-region-render/_fetchers/__init__.py
skills/locuscompare-region-render/_fetchers/gencode_ondemand.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 25
ENSEMBL_REST_BASE = "https://rest.ensembl.org" - Network accessline 25
ENSEMBL_REST_BASE = "https://rest.ensembl.org" - Access to secretsline 36
[Credential-related source omitted] - Access to secretsline 36
[Credential-related source omitted] - Network accessline 92
params = {"feature": ["gene", "exon"]} headers = {"Accept": "application/json"} resp = requests.get(url, params=params, headers=headers, timeout=timeout_s) - Network accessline 92
params = {"feature": ["gene", "exon"]} headers = {"Accept": "application/json"} resp = requests.get(url, params=params, headers=headers, timeout=timeout_s) - Network accessline 93
headers = {"Accept": "application/json"} resp = requests.get(url, params=params, headers=headers, timeout=timeout_s) resp.raise_for_status() - Network accessline 93
headers = {"Accept": "application/json"} resp = requests.get(url, params=params, headers=headers, timeout=timeout_s) resp.raise_for_status() - Network accessline 94
resp = requests.get(url, params=params, headers=headers, timeout=timeout_s) - Network accessline 94
resp = requests.get(url, params=params, headers=headers, timeout=timeout_s)
skills/locuscompare-region-render/_prefetched.py
skills/locuscompare-region-render/_region_harmonise.py
skills/locuscompare-region-render/_wald_ratio_types.py
skills/locuscompare-region-render/cli.py
skills/locuscompare-region-render/commands.sh
skills/locuscompare-region-render/examples/01_synthetic_demo/generate_synthetic_fixtures.py
skills/locuscompare-region-render/examples/05_sqtl_sort1_liver_txrev/README.md
- Network accessline 70
- **Exposure**: eQTL Catalogue v7+ dataset `QTD000269` (GTEx liver txrev / transcript-usage QTL). Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15. - Network accessline 70
- **Exposure**: eQTL Catalogue v7+ dataset `QTD000269` (GTEx liver txrev / transcript-usage QTL). Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15. - Network accessline 71
txrev / transcript-usage QTL). Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15. - **Outcome**: GWAS Catalog harmonised `GCST90269602` - Network accessline 71
txrev / transcript-usage QTL). Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15. - **Outcome**: GWAS Catalog harmonised `GCST90269602` - Network accessline 72
https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15. - Network accessline 72
https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15.
skills/locuscompare-region-render/examples/06_sceqtl_sort1_onek1k_cd14_mono/README.md
- Network accessline 29
OneK1K PBMC cell-type datasets because monocytes have non-trivial baseline SORT1 expression. Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on - Network accessline 29
OneK1K PBMC cell-type datasets because monocytes have non-trivial baseline SORT1 expression. Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on - Network accessline 30
baseline SORT1 expression. Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15. - Network accessline 30
baseline SORT1 expression. Verified live against https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on 2026-05-15. - Network accessline 31
https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on - Network accessline 31
https://www.ebi.ac.uk/eqtl/api/v2/datasets/?size=1000 on
skills/locuscompare-region-render/examples/07_pqtl_sort1_ukbppp_eur/README.md
skills/locuscompare-region-render/examples/recipes/finngen_direct/README.md
- Network accessline 7
FinnGen direct download: <https://finngen.gitbook.io/documentation/data-download> - Network accessline 7
FinnGen direct download: <https://finngen.gitbook.io/documentation/data-download> - Network accessline 10
- **Coordinate system**: GRCh38 (since R6 onwards) - **License**: open-access for sumstats since FinnGen R12; check the current release's data-use agreement at <https://www.finngen.fi/en/access_results> - Network accessline 10
- **Coordinate system**: GRCh38 (since R6 onwards) - **License**: open-access for sumstats since FinnGen R12; check the current release's data-use agreement at <https://www.finngen.fi/en/access_results> - Network accessline 11
- **License**: open-access for sumstats since FinnGen R12; check the current release's data-use agreement at <https://www.finngen.fi/en/access_results> - **Auth**: none for sumstats (was registration-gated until R11; relaxed in R12) - Network accessline 11
- **License**: open-access for sumstats since FinnGen R12; check the current release's data-use agreement at <https://www.finngen.fi/en/access_results> - **Auth**: none for sumstats (was registration-gated until R11; relaxed in R12) - Network accessline 12
release's data-use agreement at <https://www.finngen.fi/en/access_results> - Network accessline 12
release's data-use agreement at <https://www.finngen.fi/en/access_results> - Network accessline 21
# 1. Download a phenotype (e.g. heart failure I9_HEARTFAIL) wget https://storage.googleapis.com/finngen-public-data-r12/summary_stats/finngen_R12_I9_HEARTFAIL.gz - Network accessline 21
# 1. Download a phenotype (e.g. heart failure I9_HEARTFAIL) wget https://storage.googleapis.com/finngen-public-data-r12/summary_stats/finngen_R12_I9_HEARTFAIL.gz - Network accessline 22
wget https://storage.googleapis.com/finngen-public-data-r12/summary_stats/finngen_R12_I9_HEARTFAIL.gz - Network accessline 22
wget https://storage.googleapis.com/finngen-public-data-r12/summary_stats/finngen_R12_I9_HEARTFAIL.gz
skills/locuscompare-region-render/examples/recipes/finngen_direct/harmonise.sh
- Executable scriptline 1
#!/usr/bin/env bash - Executable scriptline 1
#!/usr/bin/env bash - Network accessline 15
# FinnGen R12 native columns (per https://finngen.gitbook.io/documentation/data-download): - Network accessline 15
# FinnGen R12 native columns (per https://finngen.gitbook.io/documentation/data-download):
skills/locuscompare-region-render/examples/recipes/gtex_v10_direct/README.md
- Network accessline 8
GTEx v10: <https://gtexportal.org/home/datasets> - Network accessline 8
GTEx v10: <https://gtexportal.org/home/datasets> - Network accessline 10
- **Format**: bgzip-compressed TSV per (tissue × molecular feature) - **Coordinate system**: GRCh38, GENCODE v39 - **License**: open-access; cite per <https://gtexportal.org/home/license> - Network accessline 10
- **Format**: bgzip-compressed TSV per (tissue × molecular feature) - **Coordinate system**: GRCh38, GENCODE v39 - **License**: open-access; cite per <https://gtexportal.org/home/license> - Network accessline 11
- **Coordinate system**: GRCh38, GENCODE v39 - **License**: open-access; cite per <https://gtexportal.org/home/license> - **Auth**: none for the bulk cis-eQTL files - Network accessline 11
- **Coordinate system**: GRCh38, GENCODE v39 - **License**: open-access; cite per <https://gtexportal.org/home/license> - **Auth**: none for the bulk cis-eQTL files - Network accessline 12
- **License**: open-access; cite per <https://gtexportal.org/home/license> - Network accessline 12
- **License**: open-access; cite per <https://gtexportal.org/home/license>
skills/locuscompare-region-render/examples/recipes/gtex_v10_direct/harmonise.sh
skills/locuscompare-region-render/examples/recipes/pan_ukbb_direct/README.md
- Network accessline 7
Pan-UKBB FTP: <https://pan-dev.ukbb.broadinstitute.org/downloads> - Network accessline 7
Pan-UKBB FTP: <https://pan-dev.ukbb.broadinstitute.org/downloads> - Network accessline 9
- **Format**: tab-separated, bgzip + tabix; per-phenotype + per-ancestry files - **Coordinate system**: GRCh38 - **License**: open-access; cite per <https://pan.ukbb.broadinstitute.org/> - Network accessline 9
- **Format**: tab-separated, bgzip + tabix; per-phenotype + per-ancestry files - **Coordinate system**: GRCh38 - **License**: open-access; cite per <https://pan.ukbb.broadinstitute.org/> - Network accessline 10
- **Coordinate system**: GRCh38 - **License**: open-access; cite per <https://pan.ukbb.broadinstitute.org/> - **Auth**: none for the bulk sumstats files - Network accessline 10
- **Coordinate system**: GRCh38 - **License**: open-access; cite per <https://pan.ukbb.broadinstitute.org/> - **Auth**: none for the bulk sumstats files - Network accessline 11
- **License**: open-access; cite per <https://pan.ukbb.broadinstitute.org/> - Network accessline 11
- **License**: open-access; cite per <https://pan.ukbb.broadinstitute.org/> - Network accessline 29
# Download (e.g. cholesterol biomarker 30760) wget https://pan-ukb-us-east-1.s3.amazonaws.com/sumstats_release/biomarkers-30760-both_sexes-irnt.tsv.bgz - Network accessline 29
# Download (e.g. cholesterol biomarker 30760) wget https://pan-ukb-us-east-1.s3.amazonaws.com/sumstats_release/biomarkers-30760-both_sexes-irnt.tsv.bgz - Network accessline 30
wget https://pan-ukb-us-east-1.s3.amazonaws.com/sumstats_release/biomarkers-30760-both_sexes-irnt.tsv.bgz - Network accessline 30
wget https://pan-ukb-us-east-1.s3.amazonaws.com/sumstats_release/biomarkers-30760-both_sexes-irnt.tsv.bgz - Network accessline 31
wget https://pan-ukb-us-east-1.s3.amazonaws.com/sumstats_release/biomarkers-30760-both_sexes-irnt.tsv.bgz.tbi - Network accessline 31
wget https://pan-ukb-us-east-1.s3.amazonaws.com/sumstats_release/biomarkers-30760-both_sexes-irnt.tsv.bgz.tbi - Network accessline 70
> Pan-UKB team. (2020). *Pan-UK Biobank.* > <https://pan.ukbb.broadinstitute.org> - Network accessline 70
> Pan-UKB team. (2020). *Pan-UK Biobank.* > <https://pan.ukbb.broadinstitute.org> - Network accessline 71
> <https://pan.ukbb.broadinstitute.org> - Network accessline 71
> <https://pan.ukbb.broadinstitute.org>
skills/locuscompare-region-render/examples/recipes/pan_ukbb_direct/harmonise.sh
skills/locuscompare-region-render/examples/recipes/ukb_ppp_pqtl/README.md
- Network accessline 8
UKB-PPP: <https://www.synapse.org/Synapse:syn51365303> (Synapse-hosted) - Network accessline 8
UKB-PPP: <https://www.synapse.org/Synapse:syn51365303> (Synapse-hosted) - Network accessline 21
1. Apply for UKB access at <https://www.ukbiobank.ac.uk/enable-your-research> - Network accessline 21
1. Apply for UKB access at <https://www.ukbiobank.ac.uk/enable-your-research> - Network accessline 22
2. Apply for UKB-PPP-specific access at <https://www.synapse.org/Synapse:syn51365303> 3. Set up Synapse credentials: `pip install 'synapseclient>=4.0,<5' && synapse login` 4. Download a protein's pQTL TSV: `synapse get syn51365303` (browse - Network accessline 22
2. Apply for UKB-PPP-specific access at <https://www.synapse.org/Synapse:syn51365303> 3. Set up Synapse credentials: `pip install 'synapseclient>=4.0,<5' && synapse login` 4. Download a protein's pQTL TSV: `synapse get syn51365303` (browse
skills/locuscompare-region-render/examples/recipes/ukb_ppp_pqtl/harmonise.sh
skills/locuscompare-region-render/locuscompare_region_render.py
skills/locuscompare-region-render/regional_plot.py
skills/locuscompare-region-render/tests/__init__.py
skills/locuscompare-region-render/tests/test_cli.py
skills/locuscompare-region-render/tests/test_effect_size_panel_odds_ratio.py
skills/locuscompare-region-render/tests/test_gencode_ondemand.py
skills/locuscompare-region-render/tests/test_gene_track_xlim.py
skills/locuscompare-region-render/tests/test_generate_synthetic_fixtures.py
skills/locuscompare-region-render/tests/test_golden_parity_sort1_dual_modality.py
skills/locuscompare-region-render/tests/test_live_locuscompare_region_render.py
skills/locuscompare-region-render/tests/test_locuscompare_region_render.py
skills/locuscompare-region-render/tests/test_pqtl_caption_n.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 32
n_samples=n_max, synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", - Network accessline 32
n_samples=n_max, synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", - Network accessline 33
synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", n_samples_min=n_min, - Network accessline 33
synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", n_samples_min=n_min, - Network accessline 34
source_url="https://www.synapse.org/Synapse:syn52362400", - Network accessline 34
source_url="https://www.synapse.org/Synapse:syn52362400",
skills/locuscompare-region-render/tests/test_prefetched.py
skills/locuscompare-region-render/tests/test_regional_plot.py
skills/locuscompare-region-render/tests/test_wald_ratio_types.py
skills/marker-dominance-mapper/SKILL.md
- Network accessline 43
always: false emoji: "🗺<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio - Network accessline 43
always: false emoji: "🗺<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio - Network accessline 44
emoji: "🗺<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 44
emoji: "🗺<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 45
homepage: https://github.com/ClawBio/ClawBio - Network accessline 45
homepage: https://github.com/ClawBio/ClawBio
skills/marker-dominance-mapper/marker_dominance_mapper.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 113
max_y = max(float(spot["y"]) for spot in spots) or 1.0 elements = [ '<svg xmlns="http://www.w3.org/2000/svg" width="420" height="320" viewBox="0 0 420 320">', - Network accessline 113
max_y = max(float(spot["y"]) for spot in spots) or 1.0 elements = [ '<svg xmlns="http://www.w3.org/2000/svg" width="420" height="320" viewBox="0 0 420 320">', - Network accessline 114
elements = [ '<svg xmlns="http://www.w3.org/2000/svg" width="420" height="320" viewBox="0 0 420 320">', '<rect width="420" height="320" fill="#ffffff"/>', - Network accessline 114
elements = [ '<svg xmlns="http://www.w3.org/2000/svg" width="420" height="320" viewBox="0 0 420 320">', '<rect width="420" height="320" fill="#ffffff"/>', - Network accessline 115
'<svg xmlns="http://www.w3.org/2000/svg" width="420" height="320" viewBox="0 0 420 320">', - Network accessline 115
'<svg xmlns="http://www.w3.org/2000/svg" width="420" height="320" viewBox="0 0 420 320">',
skills/marker-dominance-mapper/tests/test_marker_dominance_mapper.py
skills/mendelian-randomisation/SKILL.md
- Network accessline 50
always: false emoji: 🫛 homepage: https://github.com/ClawBio/ClawBio - Network accessline 50
always: false emoji: 🫛 homepage: https://github.com/ClawBio/ClawBio - Network accessline 51
emoji: 🫛 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 51
emoji: 🫛 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 52
homepage: https://github.com/ClawBio/ClawBio - Network accessline 52
homepage: https://github.com/ClawBio/ClawBio - Network accessline 289
- [Burgess et al. (2013)](https://pubmed.ncbi.nlm.nih.gov/24114802/) — IVW method. *Genet Epidemiol* 37:658–665 - Network accessline 289
- [Burgess et al. (2013)](https://pubmed.ncbi.nlm.nih.gov/24114802/) — IVW method. *Genet Epidemiol* 37:658–665 - Network accessline 290
- [Bowden et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/26050253/) — MR-Egger. *Int J Epidemiol* 44:512–525 - Network accessline 290
- [Bowden et al. (2015)](https://pubmed.ncbi.nlm.nih.gov/26050253/) — MR-Egger. *Int J Epidemiol* 44:512–525 - Network accessline 291
- [Bowden et al. (2016)](https://pubmed.ncbi.nlm.nih.gov/27061298/) — Weighted median. *Genet Epidemiol* 40:304–314 - Network accessline 291
- [Bowden et al. (2016)](https://pubmed.ncbi.nlm.nih.gov/27061298/) — Weighted median. *Genet Epidemiol* 40:304–314 - Network accessline 292
- [Hartwig et al. (2017)](https://pubmed.ncbi.nlm.nih.gov/29040600/) — Weighted mode. *Int J Epidemiol* 46:1985–1998 - Network accessline 292
- [Hartwig et al. (2017)](https://pubmed.ncbi.nlm.nih.gov/29040600/) — Weighted mode. *Int J Epidemiol* 46:1985–1998 - Network accessline 293
- [Verbanck et al. (2018)](https://pubmed.ncbi.nlm.nih.gov/29686387/) — MR-PRESSO. *Nature Genetics* 50:693–698 - Network accessline 293
- [Verbanck et al. (2018)](https://pubmed.ncbi.nlm.nih.gov/29686387/) — MR-PRESSO. *Nature Genetics* 50:693–698 - Network accessline 294
- [Hemani et al. (2017)](https://pubmed.ncbi.nlm.nih.gov/29149188/) — Steiger test. *PLOS Genetics* 13:e1007081 - Network accessline 294
- [Hemani et al. (2017)](https://pubmed.ncbi.nlm.nih.gov/29149188/) — Steiger test. *PLOS Genetics* 13:e1007081 - Network accessline 295
- [Skrivankova et al. (2021)](https://pubmed.ncbi.nlm.nih.gov/34702754/) — STROBE-MR. *BMJ* 375:n2233 - Network accessline 295
- [Skrivankova et al. (2021)](https://pubmed.ncbi.nlm.nih.gov/34702754/) — STROBE-MR. *BMJ* 375:n2233 - Network accessline 296
- [Staiger & Stock (1997)](https://doi.org/10.2307/2171753) — Weak instruments. *Econometrica* 65:557–586 - Network accessline 296
- [Staiger & Stock (1997)](https://doi.org/10.2307/2171753) — Weak instruments. *Econometrica* 65:557–586
skills/mendelian-randomisation/mendelian_randomisation.py
skills/mendelian-randomisation/tests/__init__.py
skills/mendelian-randomisation/tests/test_mendelian_randomisation.py
skills/methylation-clock/SKILL.md
- Network accessline 20
always: false emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio - Network accessline 20
always: false emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio - Network accessline 21
emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 21
emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 22
homepage: https://github.com/ClawBio/ClawBio - Network accessline 22
homepage: https://github.com/ClawBio/ClawBio
skills/methylation-clock/methylation_clock.py
skills/methylation-clock/tests/test_methylation_clock.py
skills/methylation-clock/tests/test_sha256_delegation.py
skills/multiqc-reporter/SKILL.md
- Network accessline 50
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 50
always: false emoji: 📊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 51
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 51
emoji: 📊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 52
homepage: https://github.com/ClawBio/ClawBio - Network accessline 52
homepage: https://github.com/ClawBio/ClawBio - Network accessline 249
- Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. *Bioinformatics* (2016). https://doi.org/10.1093/bioinformatics/btw354 - Network accessline 249
- Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: Summarize analysis results for multiple tools and samples in a single report. *Bioinformatics* (2016). https://doi.org/10.1093/bioinformatics/btw354
skills/multiqc-reporter/multiqc_reporter.py
skills/multiqc-reporter/tests/__init__.py
skills/multiqc-reporter/tests/test_multiqc_reporter.py
skills/ncbi-datasets/SKILL.md
- Network accessline 13
always: false emoji: 🧬 homepage: https://www.ncbi.nlm.nih.gov/datasets/ - Network accessline 13
always: false emoji: 🧬 homepage: https://www.ncbi.nlm.nih.gov/datasets/ - Network accessline 14
emoji: 🧬 homepage: https://www.ncbi.nlm.nih.gov/datasets/ os: - Network accessline 14
emoji: 🧬 homepage: https://www.ncbi.nlm.nih.gov/datasets/ os: - Network accessline 15
homepage: https://www.ncbi.nlm.nih.gov/datasets/ - Network accessline 15
homepage: https://www.ncbi.nlm.nih.gov/datasets/ - Network accessline 206
**Install via direct download (macOS / Linux / Windows):** > See [`references/ncbi-datasets.md § Installation`](references/ncbi-datasets.md#installation) for curl commands, or visit the [official NCBI install guide](https://www.ncbi.nlm.nih - Network accessline 206
**Install via direct download (macOS / Linux / Windows):** > See [`references/ncbi-datasets.md § Installation`](references/ncbi-datasets.md#installation) for curl commands, or visit the [official NCBI install guide](https://www.ncbi.nlm.nih - Network accessline 207
> See [`references/ncbi-datasets.md § Installation`](references/ncbi-datasets.md#installation) for curl commands, or visit the [official NCBI install guide](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/). - Network accessline 207
> See [`references/ncbi-datasets.md § Installation`](references/ncbi-datasets.md#installation) for curl commands, or visit the [official NCBI install guide](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/). - Network accessline 212
## Error handling - Attempt to use --help to retrieve command usage and parameter descriptions - Refer to the [NCBI Datasets documentation](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/) for further troubleshooting and guidance - Network accessline 212
## Error handling - Attempt to use --help to retrieve command usage and parameter descriptions - Refer to the [NCBI Datasets documentation](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/) for further troubleshooting and guidance - Network accessline 214
- Refer to the [NCBI Datasets documentation](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/) for further troubleshooting and guidance - Network accessline 214
- Refer to the [NCBI Datasets documentation](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/) for further troubleshooting and guidance - Network accessline 227
- **NCBI Datasets CLI** — Sayers et al. (2022) "Database resources of the National Center for Biotechnology Information." *Nucleic Acids Research*, 50(D1): D20–D26. https://doi.org/10.1093/nar/gkab1112 - Network accessline 227
- **NCBI Datasets CLI** — Sayers et al. (2022) "Database resources of the National Center for Biotechnology Information." *Nucleic Acids Research*, 50(D1): D20–D26. https://doi.org/10.1093/nar/gkab1112 - Network accessline 228
- **NCBI Genome Database** — https://www.ncbi.nlm.nih.gov/genome/ - Network accessline 228
- **NCBI Genome Database** — https://www.ncbi.nlm.nih.gov/genome/ - Network accessline 229
- **NCBI Datasets Documentation** - https://www.ncbi.nlm.nih.gov/datasets/docs/v2/ - Network accessline 229
- **NCBI Datasets Documentation** - https://www.ncbi.nlm.nih.gov/datasets/docs/v2/ - Network accessline 230
- **RefSeq** — O'Leary et al. (2016) "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." *Nucleic Acids Research*, 44(D1): D733–D745. https://doi.org/10.1093/nar/gkv1189 - Network accessline 230
- **RefSeq** — O'Leary et al. (2016) "Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation." *Nucleic Acids Research*, 44(D1): D733–D745. https://doi.org/10.1093/nar/gkv1189 - Network accessline 231
- **NCBI Gene** — https://www.ncbi.nlm.nih.gov/gene/ - Network accessline 231
- **NCBI Gene** — https://www.ncbi.nlm.nih.gov/gene/ - Network accessline 232
- **NCBI Taxonomy** — Schoch et al. (2020) "NCBI Taxonomy: a comprehensive update on curation, resources and tools." *Database*, 2020: baaa062. https://doi.org/10.1093/database/baaa062 - Network accessline 232
- **NCBI Taxonomy** — Schoch et al. (2020) "NCBI Taxonomy: a comprehensive update on curation, resources and tools." *Database*, 2020: baaa062. https://doi.org/10.1093/database/baaa062 - Network accessline 233
- **NCBI Virus** — Hatcher et al. (2017) "Virus Variation Resource – improved response to emergent viral outbreaks." *Nucleic Acids Research*, 45(D1): D482–D490. https://doi.org/10.1093/nar/gkw1065 - Network accessline 233
- **NCBI Virus** — Hatcher et al. (2017) "Virus Variation Resource – improved response to emergent viral outbreaks." *Nucleic Acids Research*, 45(D1): D482–D490. https://doi.org/10.1093/nar/gkw1065
skills/ncbi-datasets/references/ncbi-datasets.md
- Network accessline 26
### curl — macOS (Universal) - Network accessline 26
### curl — macOS (Universal) - Network accessline 28
curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/datasets' - Network accessline 28
curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/datasets' - Network accessline 29
curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/dataformat' - Network accessline 29
curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/mac/dataformat' - Network accessline 33
### curl — Linux (AMD64) - Network accessline 33
### curl — Linux (AMD64) - Network accessline 35
curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets' - Network accessline 35
curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets' - Network accessline 36
curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat' - Network accessline 36
curl -o dataformat 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat' - Network accessline 40
### curl — Windows (64-bit) - Network accessline 40
### curl — Windows (64-bit) - Network accessline 42
curl -o datasets.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/datasets.exe" - Network accessline 42
curl -o datasets.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/datasets.exe" - Network accessline 43
curl -o dataformat.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/dataformat.exe" - Network accessline 43
curl -o dataformat.exe "https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/win64/dataformat.exe"
skills/nfcore-rnaseq-wrapper/CHANGELOG.md
- Network accessline 3
All notable changes to the `nfcore-rnaseq-wrapper` ClawBio skill are documented here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 3
All notable changes to the `nfcore-rnaseq-wrapper` ClawBio skill are documented here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 4
here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 4
here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 301
verbatim across the three wrappers. - **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now - Network accessline 301
verbatim across the three wrappers. - **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now - Network accessline 302
- **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now rejected at preflight (`REMOTE_INPUT_NOT_ALLOWED`) unless the flag is passe - Network accessline 302
- **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now rejected at preflight (`REMOTE_INPUT_NOT_ALLOWED`) unless the flag is passe - Network accessline 303
inputs and reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now - Network accessline 303
inputs and reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now
skills/nfcore-rnaseq-wrapper/SKILL.md
- Network accessline 55
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 55
always: false emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 56
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 56
emoji: "🧬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 57
homepage: https://github.com/ClawBio/ClawBio - Network accessline 57
homepage: https://github.com/ClawBio/ClawBio - Network accessline 233
Key methods: - Local samplesheet paths are resolved against the samplesheet directory and written as absolute POSIX paths; remote URIs (`s3://`, `https://`, ... — only accepted with `--allow-remote-inputs`) are passed through unchanged. - Network accessline 233
Key methods: - Local samplesheet paths are resolved against the samplesheet directory and written as absolute POSIX paths; remote URIs (`s3://`, `https://`, ... — only accepted with `--allow-remote-inputs`) are passed through unchanged. - Network accessline 234
- Local samplesheet paths are resolved against the samplesheet directory and written as absolute POSIX paths; remote URIs (`s3://`, `https://`, ... — only accepted with `--allow-remote-inputs`) are passed through unchanged. - Network accessline 234
- Local samplesheet paths are resolved against the samplesheet directory and written as absolute POSIX paths; remote URIs (`s3://`, `https://`, ... — only accepted with `--allow-remote-inputs`) are passed through unchanged. - Network accessline 306
- FASTQ basenames cannot contain whitespace even though parent directories may. - FASTQ basenames must end in `.fq`, `.fastq`, `.fq.gz`, or `.fastq.gz` (all four are accepted by the nf-core/rnaseq schema). Only the basename must be whitespa - Network accessline 306
- FASTQ basenames cannot contain whitespace even though parent directories may. - FASTQ basenames must end in `.fq`, `.fastq`, `.fq.gz`, or `.fastq.gz` (all four are accepted by the nf-core/rnaseq schema). Only the basename must be whitespa - Network accessline 307
- FASTQ basenames must end in `.fq`, `.fastq`, `.fq.gz`, or `.fastq.gz` (all four are accepted by the nf-core/rnaseq schema). Only the basename must be whitespace-free; parent directory paths may contain spaces. - FASTQ and BAM samplesheet - Network accessline 307
- FASTQ basenames must end in `.fq`, `.fastq`, `.fq.gz`, or `.fastq.gz` (all four are accepted by the nf-core/rnaseq schema). Only the basename must be whitespace-free; parent directory paths may contain spaces. - FASTQ and BAM samplesheet - Network accessline 308
- FASTQ and BAM samplesheet entries may be local paths or remote URIs such as `s3://...`/`https://...`. Local paths are normalized and existence-checked; remote URIs are preserved unchanged and left for Nextflow to stage. - Network accessline 308
- FASTQ and BAM samplesheet entries may be local paths or remote URIs such as `s3://...`/`https://...`. Local paths are normalized and existence-checked; remote URIs are preserved unchanged and left for Nextflow to stage. - Network accessline 309
- `--genome` may be combined with additive annotation/transcriptome overrides (`--gtf` *or* `--gff`, `--gene-bed`, `--transcript-fasta`, `--additional-fasta`, `--splicesites`, `--salmon-index`, `--kallisto-index`) — this matches nf-core/rna - Network accessline 309
- `--genome` may be combined with additive annotation/transcriptome overrides (`--gtf` *or* `--gff`, `--gene-bed`, `--transcript-fasta`, `--additional-fasta`, `--splicesites`, `--salmon-index`, `--kallisto-index`) — this matches nf-core/rna - Network accessline 310
- GENCODE autodetection (setting `gencode: true` from `gene_type`/`havana_gene` markers in the GTF) only inspects **local** `--gtf` files; for remote (`s3://`/`https://`) GTFs it is skipped silently — pass `--gencode` explicitly in that cas - Network accessline 310
- GENCODE autodetection (setting `gencode: true` from `gene_type`/`havana_gene` markers in the GTF) only inspects **local** `--gtf` files; for remote (`s3://`/`https://`) GTFs it is skipped silently — pass `--gencode` explicitly in that cas - Network accessline 321
- A sibling `../rnaseq` checkout is auto-detected and used, but its `manifest.version` must be `3.26.0` (the version this wrapper's validations are pinned to). A different version is rejected unless `--allow-pipeline-version-override` is pa - Network accessline 321
- A sibling `../rnaseq` checkout is auto-detected and used, but its `manifest.version` must be `3.26.0` (the version this wrapper's validations are pinned to). A different version is rejected unless `--allow-pipeline-version-override` is pa - Network accessline 322
- `--rseqc-modules` is validated against the eight nf-core/rnaseq 3.26.0 module names; a typo is rejected at preflight instead of failing later inside Nextflow. - `--contaminant-screening kraken2`/`kraken2_bracken` requires `--kraken-db`, a - Network accessline 322
- `--rseqc-modules` is validated against the eight nf-core/rnaseq 3.26.0 module names; a typo is rejected at preflight instead of failing later inside Nextflow. - `--contaminant-screening kraken2`/`kraken2_bracken` requires `--kraken-db`, a - Network accessline 323
- `--contaminant-screening kraken2`/`kraken2_bracken` requires `--kraken-db`, and `--contaminant-screening sylph` requires `--sylph-db`; local database paths are existence-checked before Nextflow starts, while URI schemes such as `s3://` an - Network accessline 323
- `--contaminant-screening kraken2`/`kraken2_bracken` requires `--kraken-db`, and `--contaminant-screening sylph` requires `--sylph-db`; local database paths are existence-checked before Nextflow starts, while URI schemes such as `s3://` an - Network accessline 376
- [nf-core/rnaseq 3.26.0](https://nf-co.re/rnaseq/3.26.0) - Network accessline 376
- [nf-core/rnaseq 3.26.0](https://nf-co.re/rnaseq/3.26.0) - Network accessline 377
- [nf-core/rnaseq usage](https://nf-co.re/rnaseq/3.26.0/docs/usage/) - Network accessline 377
- [nf-core/rnaseq usage](https://nf-co.re/rnaseq/3.26.0/docs/usage/) - Network accessline 378
- [nf-core/rnaseq parameters](https://nf-co.re/rnaseq/3.26.0/parameters/) - Network accessline 378
- [nf-core/rnaseq parameters](https://nf-co.re/rnaseq/3.26.0/parameters/) - Network accessline 379
- [nf-core/rnaseq output](https://nf-co.re/rnaseq/3.26.0/docs/output/) - Network accessline 379
- [nf-core/rnaseq output](https://nf-co.re/rnaseq/3.26.0/docs/output/) - Network accessline 380
- [Nextflow](https://www.nextflow.io/) - Network accessline 380
- [Nextflow](https://www.nextflow.io/) - Network accessline 381
- [STAR](https://github.com/alexdobin/STAR) - Network accessline 381
- [STAR](https://github.com/alexdobin/STAR) - Network accessline 382
- [Salmon](https://salmon.readthedocs.io/) - Network accessline 382
- [Salmon](https://salmon.readthedocs.io/) - Network accessline 383
- [RSEM](https://github.com/deweylab/RSEM) - Network accessline 383
- [RSEM](https://github.com/deweylab/RSEM) - Network accessline 384
- [HISAT2](https://daehwankimlab.github.io/hisat2/) - Network accessline 384
- [HISAT2](https://daehwankimlab.github.io/hisat2/) - Network accessline 385
- [Bowtie2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml) - Network accessline 385
- [Bowtie2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
skills/nfcore-rnaseq-wrapper/_isolated_imports.py
skills/nfcore-rnaseq-wrapper/command_builder.py
skills/nfcore-rnaseq-wrapper/errors.py
skills/nfcore-rnaseq-wrapper/executor.py
skills/nfcore-rnaseq-wrapper/nfcore_rnaseq_wrapper.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 161
help=( "Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 161
help=( "Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 162
"Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " "genetic data and references stay on the local machine. When enab - Network accessline 162
"Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " "genetic data and references stay on the local machine. When enab - Network accessline 163
"https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 163
"https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 1307
nf-core's guidance is that ``resourceLimits`` should match the machine's maximum (https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Unlike the - Network accessline 1307
nf-core's guidance is that ``resourceLimits`` should match the machine's maximum (https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Unlike the - Network accessline 1308
(https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Unlike the - Network accessline 1308
(https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Unlike the - Network accessline 1339
"// does not abort real runs whose production requirements exceed this machine.\n" "// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-f - Network accessline 1339
"// does not abort real runs whose production requirements exceed this machine.\n" "// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-f - Network accessline 1340
"// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" "process {\n" - Network accessline 1340
"// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" "process {\n" - Network accessline 1341
"// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" - Network accessline 1341
"// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n"
skills/nfcore-rnaseq-wrapper/outputs_parser.py
skills/nfcore-rnaseq-wrapper/params_builder.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 286
"""Expand to absolute POSIX path, but pass URI schemes (s3://, http://) through unchanged.""" - Network accessline 286
"""Expand to absolute POSIX path, but pass URI schemes (s3://, http://) through unchanged."""
skills/nfcore-rnaseq-wrapper/pipeline_source.py
skills/nfcore-rnaseq-wrapper/preflight.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 509
"""Local-first by default: reject remote samplesheet inputs and reference paths (s3://, gs://, https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in - Network accessline 509
"""Local-first by default: reject remote samplesheet inputs and reference paths (s3://, gs://, https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in - Network accessline 510
(s3://, gs://, https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in - Network accessline 510
(s3://, gs://, https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in - Access to secretsline 559
[Credential-related source omitted] - Access to secretsline 559
[Credential-related source omitted] - Access to secretsline 575
[Credential-related source omitted] - Access to secretsline 575
[Credential-related source omitted] - Network accessline 1073
# URI scheme (https://, s3://, gs://, ftp://) — existence check not applicable; - Network accessline 1073
# URI scheme (https://, s3://, gs://, ftp://) — existence check not applicable;
skills/nfcore-rnaseq-wrapper/provenance.py
skills/nfcore-rnaseq-wrapper/remap_paths.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 6
reference/index paths (--fasta, --gtf, --star-index, etc.) are stored as absolute paths (required by Nextflow). A run started with --allow-remote-inputs instead stores remote URIs (s3://, https://, ...), which resolve from anywhere and are - Network accessline 6
reference/index paths (--fasta, --gtf, --star-index, etc.) are stored as absolute paths (required by Nextflow). A run started with --allow-remote-inputs instead stores remote URIs (s3://, https://, ...), which resolve from anywhere and are - Network accessline 7
paths (required by Nextflow). A run started with --allow-remote-inputs instead stores remote URIs (s3://, https://, ...), which resolve from anywhere and are skipped by the remap and verify steps below. Before replaying on a different machi - Network accessline 7
paths (required by Nextflow). A run started with --allow-remote-inputs instead stores remote URIs (s3://, https://, ...), which resolve from anywhere and are skipped by the remap and verify steps below. Before replaying on a different machi - Network accessline 8
stores remote URIs (s3://, https://, ...), which resolve from anywhere and are - Network accessline 8
stores remote URIs (s3://, https://, ...), which resolve from anywhere and are - Network accessline 28
Remote URIs (s3://, https://, etc.) are recognized and skipped automatically - Network accessline 28
Remote URIs (s3://, https://, etc.) are recognized and skipped automatically - Network accessline 217
Remote URIs (s3://, https://, etc.) and bash variable references ($VAR/… - Network accessline 217
Remote URIs (s3://, https://, etc.) and bash variable references ($VAR/… - Network accessline 235
Remote URIs (s3://, https://, etc.) and bash variable references are skipped - Network accessline 235
Remote URIs (s3://, https://, etc.) and bash variable references are skipped
skills/nfcore-rnaseq-wrapper/reporting.py
skills/nfcore-rnaseq-wrapper/samplesheet_builder.py
skills/nfcore-rnaseq-wrapper/schemas.py
skills/nfcore-rnaseq-wrapper/tests/conftest.py
skills/nfcore-rnaseq-wrapper/tests/test_audit_rnaseq_hardening.py
skills/nfcore-rnaseq-wrapper/tests/test_bundle_portability.py
skills/nfcore-rnaseq-wrapper/tests/test_command_builder.py
skills/nfcore-rnaseq-wrapper/tests/test_drift_guards.py
skills/nfcore-rnaseq-wrapper/tests/test_error_codes.py
skills/nfcore-rnaseq-wrapper/tests/test_executor.py
skills/nfcore-rnaseq-wrapper/tests/test_nfcore_rnaseq_wrapper.py
skills/nfcore-rnaseq-wrapper/tests/test_outputs_parser.py
skills/nfcore-rnaseq-wrapper/tests/test_params_builder.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 481
Path(...).resolve() would turn 'https://example.org/genome.fa' into an - Network accessline 481
Path(...).resolve() would turn 'https://example.org/genome.fa' into an - Network accessline 505
@pytest.mark.parametrize("field", ["multiqc_config", "multiqc_logo", "multiqc_methods_description"]) def test_remote_multiqc_path_uri_passed_through_unchanged(tmp_path, field): uri = f"https://example.org/multiqc/{field}.yaml" - Network accessline 505
@pytest.mark.parametrize("field", ["multiqc_config", "multiqc_logo", "multiqc_methods_description"]) def test_remote_multiqc_path_uri_passed_through_unchanged(tmp_path, field): uri = f"https://example.org/multiqc/{field}.yaml" - Network accessline 506
def test_remote_multiqc_path_uri_passed_through_unchanged(tmp_path, field): uri = f"https://example.org/multiqc/{field}.yaml" params = _load_params(tmp_path, _args(**{field: uri})) - Network accessline 506
def test_remote_multiqc_path_uri_passed_through_unchanged(tmp_path, field): uri = f"https://example.org/multiqc/{field}.yaml" params = _load_params(tmp_path, _args(**{field: uri})) - Network accessline 507
uri = f"https://example.org/multiqc/{field}.yaml" - Network accessline 507
uri = f"https://example.org/multiqc/{field}.yaml"
skills/nfcore-rnaseq-wrapper/tests/test_pipeline_source.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 55
" vep_version = \"111.0-0\"\n" " custom_config_version = 'master'\n" " custom_config_base = \"https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}\"\n" - Network accessline 55
" vep_version = \"111.0-0\"\n" " custom_config_version = 'master'\n" " custom_config_base = \"https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}\"\n" - Network accessline 56
" custom_config_version = 'master'\n" " custom_config_base = \"https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}\"\n" "}\n" - Network accessline 56
" custom_config_version = 'master'\n" " custom_config_base = \"https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}\"\n" "}\n" - Network accessline 57
" custom_config_base = \"https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}\"\n" - Network accessline 57
" custom_config_base = \"https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}\"\n"
skills/nfcore-rnaseq-wrapper/tests/test_portability_remap_interpreter.py
skills/nfcore-rnaseq-wrapper/tests/test_preflight.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 493
The pipeline handles reference-less BAM reprocessing natively (e.g. using transcript info from the BAM header). The wrapper must not block this. See: https://nf-co.re/rnaseq/3.26.0/docs/usage/ (BAM input for reprocessing). - Network accessline 493
The pipeline handles reference-less BAM reprocessing natively (e.g. using transcript info from the BAM header). The wrapper must not block this. See: https://nf-co.re/rnaseq/3.26.0/docs/usage/ (BAM input for reprocessing). - Network accessline 494
transcript info from the BAM header). The wrapper must not block this. See: https://nf-co.re/rnaseq/3.26.0/docs/usage/ (BAM input for reprocessing). """ - Network accessline 494
transcript info from the BAM header). The wrapper must not block this. See: https://nf-co.re/rnaseq/3.26.0/docs/usage/ (BAM input for reprocessing). """ - Network accessline 495
See: https://nf-co.re/rnaseq/3.26.0/docs/usage/ (BAM input for reprocessing). - Network accessline 495
See: https://nf-co.re/rnaseq/3.26.0/docs/usage/ (BAM input for reprocessing). - Network accessline 1630
_mock_env(monkeypatch) cfg = tmp_path / "remote_include.config" cfg.write_text("includeConfig 'https://example.org/foo.config'\n", encoding="utf-8") - Network accessline 1630
_mock_env(monkeypatch) cfg = tmp_path / "remote_include.config" cfg.write_text("includeConfig 'https://example.org/foo.config'\n", encoding="utf-8") - Network accessline 1631
cfg = tmp_path / "remote_include.config" cfg.write_text("includeConfig 'https://example.org/foo.config'\n", encoding="utf-8") result = _run(_args(tmp_path, nextflow_config=[str(cfg)]), _samplesheet(tmp_path)) - Network accessline 1631
cfg = tmp_path / "remote_include.config" cfg.write_text("includeConfig 'https://example.org/foo.config'\n", encoding="utf-8") result = _run(_args(tmp_path, nextflow_config=[str(cfg)]), _samplesheet(tmp_path)) - Network accessline 1632
cfg.write_text("includeConfig 'https://example.org/foo.config'\n", encoding="utf-8") - Network accessline 1632
cfg.write_text("includeConfig 'https://example.org/foo.config'\n", encoding="utf-8") - Network accessline 1795
def test_remote_inputs_allowed_with_flag_warns(capsys): from argparse import Namespace as _NS preflight._check_remote_inputs(_NS(allow_remote_inputs=True), {"fastq_paths": ["https://x/n_R1.fastq.gz"]}) - Network accessline 1795
def test_remote_inputs_allowed_with_flag_warns(capsys): from argparse import Namespace as _NS preflight._check_remote_inputs(_NS(allow_remote_inputs=True), {"fastq_paths": ["https://x/n_R1.fastq.gz"]}) - Network accessline 1796
from argparse import Namespace as _NS preflight._check_remote_inputs(_NS(allow_remote_inputs=True), {"fastq_paths": ["https://x/n_R1.fastq.gz"]}) assert "--allow-remote-inputs" in capsys.readouterr().err - Network accessline 1796
from argparse import Namespace as _NS preflight._check_remote_inputs(_NS(allow_remote_inputs=True), {"fastq_paths": ["https://x/n_R1.fastq.gz"]}) assert "--allow-remote-inputs" in capsys.readouterr().err - Network accessline 1797
preflight._check_remote_inputs(_NS(allow_remote_inputs=True), {"fastq_paths": ["https://x/n_R1.fastq.gz"]}) - Network accessline 1797
preflight._check_remote_inputs(_NS(allow_remote_inputs=True), {"fastq_paths": ["https://x/n_R1.fastq.gz"]})
skills/nfcore-rnaseq-wrapper/tests/test_provenance.py
skills/nfcore-rnaseq-wrapper/tests/test_remap_paths.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 459
"python skill.py \\\n" " --fasta s3://my-bucket/genome.fa \\\n" " --gtf https://example.com/genes.gtf \\\n" - Network accessline 459
"python skill.py \\\n" " --fasta s3://my-bucket/genome.fa \\\n" " --gtf https://example.com/genes.gtf \\\n" - Network accessline 460
" --fasta s3://my-bucket/genome.fa \\\n" " --gtf https://example.com/genes.gtf \\\n" " --output /tmp/out \\\n", - Network accessline 460
" --fasta s3://my-bucket/genome.fa \\\n" " --gtf https://example.com/genes.gtf \\\n" " --output /tmp/out \\\n", - Network accessline 461
" --gtf https://example.com/genes.gtf \\\n" - Network accessline 461
" --gtf https://example.com/genes.gtf \\\n" - Network accessline 515
"""verify_paths must not report remote FASTQ/BAM URIs (s3://, https://, etc.) as - Network accessline 515
"""verify_paths must not report remote FASTQ/BAM URIs (s3://, https://, etc.) as - Network accessline 520
"sample,fastq_1,fastq_2,strandedness\n" "S1,s3://bucket/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz,auto\n" "S2,https://example.com/S2.fastq.gz,,auto\n", - Network accessline 520
"sample,fastq_1,fastq_2,strandedness\n" "S1,s3://bucket/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz,auto\n" "S2,https://example.com/S2.fastq.gz,,auto\n", - Network accessline 521
"S1,s3://bucket/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz,auto\n" "S2,https://example.com/S2.fastq.gz,,auto\n", encoding="utf-8", - Network accessline 521
"S1,s3://bucket/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz,auto\n" "S2,https://example.com/S2.fastq.gz,,auto\n", encoding="utf-8", - Network accessline 522
"S2,https://example.com/S2.fastq.gz,,auto\n", - Network accessline 522
"S2,https://example.com/S2.fastq.gz,,auto\n",
skills/nfcore-rnaseq-wrapper/tests/test_reporting.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 506
Path(value).resolve() turns 'https://example.org/genome.fa' into - Network accessline 506
Path(value).resolve() turns 'https://example.org/genome.fa' into - Network accessline 597
result = build_repro_command_args( tmp_path, args=_args(tmp_path, nextflow_config=["https://example.org/hpc.config"]) - Network accessline 597
result = build_repro_command_args( tmp_path, args=_args(tmp_path, nextflow_config=["https://example.org/hpc.config"]) - Network accessline 598
tmp_path, args=_args(tmp_path, nextflow_config=["https://example.org/hpc.config"]) - Network accessline 598
tmp_path, args=_args(tmp_path, nextflow_config=["https://example.org/hpc.config"]) - Network accessline 600
assert result["--nextflow-config"] == ["https://example.org/hpc.config"] - Network accessline 600
assert result["--nextflow-config"] == ["https://example.org/hpc.config"]
skills/nfcore-rnaseq-wrapper/tests/test_samplesheet_builder.py
skills/nfcore-rnastructurome-wrapper/SKILL.md
- Network accessline 59
always: false emoji: "🧬" homepage: https://github.com/nf-core/rnastructurome - Network accessline 59
always: false emoji: "🧬" homepage: https://github.com/nf-core/rnastructurome - Network accessline 60
emoji: "🧬" homepage: https://github.com/nf-core/rnastructurome os: - Network accessline 60
emoji: "🧬" homepage: https://github.com/nf-core/rnastructurome os: - Network accessline 61
homepage: https://github.com/nf-core/rnastructurome - Network accessline 61
homepage: https://github.com/nf-core/rnastructurome - Network accessline 229
Rendered examples of every output — `count/rfcount_summary_all_samples.tsv`, `rfnorm.log`, `rfcorrelate.log`, RDAT records, R2DT and ViennaRNA structure diagrams, IGV track screenshots, rf-jackknife/rf-eval metrics and the MultiQC sections - Network accessline 229
Rendered examples of every output — `count/rfcount_summary_all_samples.tsv`, `rfnorm.log`, `rfcorrelate.log`, RDAT records, R2DT and ViennaRNA structure diagrams, IGV track screenshots, rf-jackknife/rf-eval metrics and the MultiQC sections - Network accessline 233
All paths relative to `--outdir`. See the [1.0.0 output docs](https://nf-co.re/rnastructurome/1.0.0/docs/output/) for the full annotated layout; the parts an agent will point users to most: - Network accessline 233
All paths relative to `--outdir`. See the [1.0.0 output docs](https://nf-co.re/rnastructurome/1.0.0/docs/output/) for the full annotated layout; the parts an agent will point users to most: - Network accessline 294
- No patient data is bundled; demo mode uses public nf-core test data. - Local-first: reference and FASTQ paths passed to `--fasta`/`--gtf`/`--input` are used as given — this skill does not upload data anywhere itself. Remote URIs the user - Network accessline 294
- No patient data is bundled; demo mode uses public nf-core test data. - Local-first: reference and FASTQ paths passed to `--fasta`/`--gtf`/`--input` are used as given — this skill does not upload data anywhere itself. Remote URIs the user - Network accessline 295
- Local-first: reference and FASTQ paths passed to `--fasta`/`--gtf`/`--input` are used as given — this skill does not upload data anywhere itself. Remote URIs the user supplies (`s3://`, `https://`) are staged by Nextflow, not by this skil - Network accessline 295
- Local-first: reference and FASTQ paths passed to `--fasta`/`--gtf`/`--input` are used as given — this skill does not upload data anywhere itself. Remote URIs the user supplies (`s3://`, `https://`) are staged by Nextflow, not by this skil - Network accessline 308
2. Reproduce on `-profile test,docker` where possible, so the report contains only public nf-core test data. If the failure needs the user's own data to trigger, reduce to the smallest input that still fails (one sample, one reference). 3. - Network accessline 308
2. Reproduce on `-profile test,docker` where possible, so the report contains only public nf-core test data. If the failure needs the user's own data to trigger, reduce to the smallest input that still fails (one sample, one reference). 3. - Network accessline 309
3. Gather `.nextflow.log`, the failing task's `.command.err`/`.command.sh`, the samplesheet, and the exact `nextflow run` command plus params file — then **redact before posting**: replace sample names, `sample_group` labels, file paths, ho - Network accessline 309
3. Gather `.nextflow.log`, the failing task's `.command.err`/`.command.sh`, the samplesheet, and the exact `nextflow run` command plus params file — then **redact before posting**: replace sample names, `sample_group` labels, file paths, ho - Network accessline 310
4. Search [existing issues](https://github.com/nf-core/rnastructurome/issues) first. - Network accessline 310
4. Search [existing issues](https://github.com/nf-core/rnastructurome/issues) first. - Network accessline 329
- [nf-core/rnastructurome](https://github.com/nf-core/rnastructurome) - Network accessline 329
- [nf-core/rnastructurome](https://github.com/nf-core/rnastructurome) - Network accessline 330
- [nf-core/rnastructurome usage (1.0.0)](https://nf-co.re/rnastructurome/1.0.0/docs/usage/) - Network accessline 330
- [nf-core/rnastructurome usage (1.0.0)](https://nf-co.re/rnastructurome/1.0.0/docs/usage/) - Network accessline 331
- [nf-core/rnastructurome output (1.0.0)](https://nf-co.re/rnastructurome/1.0.0/docs/output/) - Network accessline 331
- [nf-core/rnastructurome output (1.0.0)](https://nf-co.re/rnastructurome/1.0.0/docs/output/) - Network accessline 332
- [Nextflow](https://www.nextflow.io/) - Network accessline 332
- [Nextflow](https://www.nextflow.io/) - Network accessline 333
- [RNA Framework](https://rnaframework.readthedocs.io/) — Incarnato lab - Network accessline 333
- [RNA Framework](https://rnaframework.readthedocs.io/) — Incarnato lab - Network accessline 334
- [ViennaRNA](https://www.tbi.univie.ac.at/RNA/) - Network accessline 334
- [ViennaRNA](https://www.tbi.univie.ac.at/RNA/) - Network accessline 335
- [R2DT](https://github.com/RNAcentral/R2DT) - Network accessline 335
- [R2DT](https://github.com/RNAcentral/R2DT) - Network accessline 336
- [STAR](https://github.com/alexdobin/STAR) - Network accessline 336
- [STAR](https://github.com/alexdobin/STAR) - Network accessline 337
- [Bowtie2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml) - Network accessline 337
- [Bowtie2](https://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
skills/nfcore-rnastructurome-wrapper/references/parameters.md
- Network accessline 3
Generated from `nextflow_schema.json` in [nf-core/rnastructurome](https://github.com/nf-core/rnastructurome) v1.0.0. - Network accessline 3
Generated from `nextflow_schema.json` in [nf-core/rnastructurome](https://github.com/nf-core/rnastructurome) v1.0.0. - Network accessline 22
| `--gtf` | string | `—` | Path to transcript annotation GTF file. | | `--genomes` | object | `—` | Optional custom reference map keyed by organism/reference name. | | `--ensembl_base_url` | string | `https://ftp.ensembl.org/pub` | Ensembl - Network accessline 22
| `--gtf` | string | `—` | Path to transcript annotation GTF file. | | `--genomes` | object | `—` | Optional custom reference map keyed by organism/reference name. | | `--ensembl_base_url` | string | `https://ftp.ensembl.org/pub` | Ensembl - Network accessline 23
| `--genomes` | object | `—` | Optional custom reference map keyed by organism/reference name. | | `--ensembl_base_url` | string | `https://ftp.ensembl.org/pub` | Ensembl FTP base URL used when auto-resolving the reference: soft-masked geno - Network accessline 23
| `--genomes` | object | `—` | Optional custom reference map keyed by organism/reference name. | | `--ensembl_base_url` | string | `https://ftp.ensembl.org/pub` | Ensembl FTP base URL used when auto-resolving the reference: soft-masked geno - Network accessline 24
| `--ensembl_base_url` | string | `https://ftp.ensembl.org/pub` | Ensembl FTP base URL used when auto-resolving the reference: soft-masked genome FASTA + GTF (default STAR route) or cDNA FASTA (`transcriptome: true`). | - Network accessline 24
| `--ensembl_base_url` | string | `https://ftp.ensembl.org/pub` | Ensembl FTP base URL used when auto-resolving the reference: soft-masked genome FASTA + GTF (default STAR route) or cDNA FASTA (`transcriptome: true`). | - Network accessline 201
|---|---|---|---| | `--custom_config_version` | string | `master` | Git commit id for Institutional configs. | | `--custom_config_base` | string | `https://raw.githubusercontent.com/nf-core/configs/master` | Base directory for Institutional - Network accessline 201
|---|---|---|---| | `--custom_config_version` | string | `master` | Git commit id for Institutional configs. | | `--custom_config_base` | string | `https://raw.githubusercontent.com/nf-core/configs/master` | Base directory for Institutional - Network accessline 202
| `--custom_config_version` | string | `master` | Git commit id for Institutional configs. | | `--custom_config_base` | string | `https://raw.githubusercontent.com/nf-core/configs/master` | Base directory for Institutional configs. | | `--c - Network accessline 202
| `--custom_config_version` | string | `master` | Git commit id for Institutional configs. | | `--custom_config_base` | string | `https://raw.githubusercontent.com/nf-core/configs/master` | Base directory for Institutional configs. | | `--c - Network accessline 203
| `--custom_config_base` | string | `https://raw.githubusercontent.com/nf-core/configs/master` | Base directory for Institutional configs. | - Network accessline 203
| `--custom_config_base` | string | `https://raw.githubusercontent.com/nf-core/configs/master` | Base directory for Institutional configs. | - Network accessline 230
| `--multiqc_methods_description` | string | `—` | Custom MultiQC yaml file containing HTML including a methods description. | | `--validate_params` | boolean | `True` | Boolean whether to validate parameters against the schema at runtime | - Network accessline 230
| `--multiqc_methods_description` | string | `—` | Custom MultiQC yaml file containing HTML including a methods description. | | `--validate_params` | boolean | `True` | Boolean whether to validate parameters against the schema at runtime | - Network accessline 231
| `--validate_params` | boolean | `True` | Boolean whether to validate parameters against the schema at runtime | | `--pipelines_testdata_base_path` | string | `https://raw.githubusercontent.com/nf-core/test-datasets/` | Base URL or local p - Network accessline 231
| `--validate_params` | boolean | `True` | Boolean whether to validate parameters against the schema at runtime | | `--pipelines_testdata_base_path` | string | `https://raw.githubusercontent.com/nf-core/test-datasets/` | Base URL or local p - Network accessline 232
| `--pipelines_testdata_base_path` | string | `https://raw.githubusercontent.com/nf-core/test-datasets/` | Base URL or local path to location of pipeline test dataset files | - Network accessline 232
| `--pipelines_testdata_base_path` | string | `https://raw.githubusercontent.com/nf-core/test-datasets/` | Base URL or local path to location of pipeline test dataset files |
skills/nfcore-sarek-wrapper/CHANGELOG.md
- Network accessline 3
All notable changes to the `nfcore-sarek-wrapper` ClawBio skill are documented here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 3
All notable changes to the `nfcore-sarek-wrapper` ClawBio skill are documented here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 4
here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 4
here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 145
`--igenomes-base`.** nf-core/sarek's tiny test genome resolves only under the test-datasets mirror (`conf/test.config` sets `igenomes_base` to `https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/`), never the - Network accessline 145
`--igenomes-base`.** nf-core/sarek's tiny test genome resolves only under the test-datasets mirror (`conf/test.config` sets `igenomes_base` to `https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/`), never the - Network accessline 146
test-datasets mirror (`conf/test.config` sets `igenomes_base` to `https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/`), never the default `s3://ngi-igenomes` catalogue — yet it was accepted like a normal iGenomes - Network accessline 146
test-datasets mirror (`conf/test.config` sets `igenomes_base` to `https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/`), never the default `s3://ngi-igenomes` catalogue — yet it was accepted like a normal iGenomes - Network accessline 147
`https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/`), never the - Network accessline 147
`https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/`), never the - Network accessline 248
- **Remote MultiQC config/logo URIs are preserved in `params.yaml`.** A remote `--multiqc-config`/`--multiqc-logo`/`--multiqc-methods-description` URL was resolved as a local path (collapsing the scheme, e.g. `https://host/x` → - Network accessline 248
- **Remote MultiQC config/logo URIs are preserved in `params.yaml`.** A remote `--multiqc-config`/`--multiqc-logo`/`--multiqc-methods-description` URL was resolved as a local path (collapsing the scheme, e.g. `https://host/x` → - Network accessline 249
`--multiqc-config`/`--multiqc-logo`/`--multiqc-methods-description` URL was resolved as a local path (collapsing the scheme, e.g. `https://host/x` → `<cwd>/https:/host/x`); those fields now pass URIs through verbatim via - Network accessline 249
`--multiqc-config`/`--multiqc-logo`/`--multiqc-methods-description` URL was resolved as a local path (collapsing the scheme, e.g. `https://host/x` → `<cwd>/https:/host/x`); those fields now pass URIs through verbatim via - Network accessline 250
resolved as a local path (collapsing the scheme, e.g. `https://host/x` → - Network accessline 250
resolved as a local path (collapsing the scheme, e.g. `https://host/x` → - Network accessline 326
wrappers. - **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and user-supplied reference paths (`s3://`, `gs://`, `https://`, `ftp://`, - Network accessline 326
wrappers. - **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and user-supplied reference paths (`s3://`, `gs://`, `https://`, `ftp://`, - Network accessline 327
- **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and user-supplied reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now rejected at preflight (`REMOTE_INPUT_NOT_ALLOWED`) unless the - Network accessline 327
- **`--allow-remote-inputs` opt-in (local-first by default).** Remote samplesheet inputs and user-supplied reference paths (`s3://`, `gs://`, `https://`, `ftp://`, …) are now rejected at preflight (`REMOTE_INPUT_NOT_ALLOWED`) unless the - Network accessline 328
inputs and user-supplied reference paths (`s3://`, `gs://`, `https://`, `ftp://`, - Network accessline 328
inputs and user-supplied reference paths (`s3://`, `gs://`, `https://`, `ftp://`,
skills/nfcore-sarek-wrapper/SKILL.md
- Network accessline 66
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 66
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 67
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 67
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 68
homepage: https://github.com/ClawBio/ClawBio - Network accessline 68
homepage: https://github.com/ClawBio/ClawBio - Network accessline 148
The samplesheet may be `.csv`, `.tsv`, `.yaml`, `.yml`, or `.json` (CSV/TSV are delimited; YAML/JSON are a top-level list of row records). File-column values must be local paths by default (local-first): remote URLs (`https://`, `s3://`, - Network accessline 148
The samplesheet may be `.csv`, `.tsv`, `.yaml`, `.yml`, or `.json` (CSV/TSV are delimited; YAML/JSON are a top-level list of row records). File-column values must be local paths by default (local-first): remote URLs (`https://`, `s3://`, - Network accessline 149
delimited; YAML/JSON are a top-level list of row records). File-column values must be local paths by default (local-first): remote URLs (`https://`, `s3://`, `gs://`, `ftp://`, …) — and remote reference paths — are rejected at preflight - Network accessline 149
delimited; YAML/JSON are a top-level list of row records). File-column values must be local paths by default (local-first): remote URLs (`https://`, `s3://`, `gs://`, `ftp://`, …) — and remote reference paths — are rejected at preflight - Network accessline 150
must be local paths by default (local-first): remote URLs (`https://`, `s3://`, - Network accessline 150
must be local paths by default (local-first): remote URLs (`https://`, `s3://`, - Network accessline 357
**Cross-machine / cross-OS portability.** The bundle stores absolute data/reference paths (required by Nextflow) but ships a stdlib-only `remap_paths.py` to rebase them on any host: `--old/--new` rewrites samplesheet data paths, `--refs-old - Network accessline 357
**Cross-machine / cross-OS portability.** The bundle stores absolute data/reference paths (required by Nextflow) but ships a stdlib-only `remap_paths.py` to rebase them on any host: `--old/--new` rewrites samplesheet data paths, `--refs-old - Network accessline 432
- nf-core/sarek 3.8.1: https://github.com/nf-core/sarek - Network accessline 432
- nf-core/sarek 3.8.1: https://github.com/nf-core/sarek - Network accessline 433
- GATK Best Practices: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows - Network accessline 433
- GATK Best Practices: https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows - Network accessline 434
- VEP: https://www.ensembl.org/info/docs/tools/vep/index.html - Network accessline 434
- VEP: https://www.ensembl.org/info/docs/tools/vep/index.html
skills/nfcore-sarek-wrapper/_isolated_imports.py
skills/nfcore-sarek-wrapper/command_builder.py
skills/nfcore-sarek-wrapper/errors.py
skills/nfcore-sarek-wrapper/executor.py
skills/nfcore-sarek-wrapper/nfcore_sarek_wrapper.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 472
help=( "Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 472
help=( "Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 473
"Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " "genetic data and references stay on the local machine. When enab - Network accessline 473
"Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " "genetic data and references stay on the local machine. When enab - Network accessline 474
"https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 474
"https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 1318
nf-core's guidance is that ``resourceLimits`` should match the machine's maximum (https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1318
nf-core's guidance is that ``resourceLimits`` should match the machine's maximum (https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1319
(https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1319
(https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1356
"// does not abort real runs whose production requirements exceed this machine.\n" "// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-f - Network accessline 1356
"// does not abort real runs whose production requirements exceed this machine.\n" "// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-f - Network accessline 1357
"// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" "process {\n" - Network accessline 1357
"// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" "process {\n" - Network accessline 1358
"// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" - Network accessline 1358
"// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n"
skills/nfcore-sarek-wrapper/outputs_parser.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 364
"""Mutect2 emits an unfiltered VCF, a filtered VCF, and several auxiliary tables/archives used by FilterMutectCalls — capture them all. See https://nf-co.re/sarek/3.8.1/docs/output/#mutect2 . - Network accessline 364
"""Mutect2 emits an unfiltered VCF, a filtered VCF, and several auxiliary tables/archives used by FilterMutectCalls — capture them all. See https://nf-co.re/sarek/3.8.1/docs/output/#mutect2 . - Network accessline 365
tables/archives used by FilterMutectCalls — capture them all. See https://nf-co.re/sarek/3.8.1/docs/output/#mutect2 . """ - Network accessline 365
tables/archives used by FilterMutectCalls — capture them all. See https://nf-co.re/sarek/3.8.1/docs/output/#mutect2 . """ - Network accessline 366
See https://nf-co.re/sarek/3.8.1/docs/output/#mutect2 . - Network accessline 366
See https://nf-co.re/sarek/3.8.1/docs/output/#mutect2 . - Network accessline 611
# ASCAT also publishes raw tumour BAF / LogR txt traces. # See https://nf-co.re/sarek/3.8.1/docs/output/#ascat - Network accessline 611
# ASCAT also publishes raw tumour BAF / LogR txt traces. # See https://nf-co.re/sarek/3.8.1/docs/output/#ascat - Network accessline 612
# See https://nf-co.re/sarek/3.8.1/docs/output/#ascat - Network accessline 612
# See https://nf-co.re/sarek/3.8.1/docs/output/#ascat
skills/nfcore-sarek-wrapper/params_builder.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 135
# freebayes_filter is `string` upstream — a vcflib/vcffilter expression # (default "30"), not an integer. See https://nf-co.re/sarek/3.8.1/parameters/ . - Network accessline 135
# freebayes_filter is `string` upstream — a vcflib/vcffilter expression # (default "30"), not an integer. See https://nf-co.re/sarek/3.8.1/parameters/ . - Network accessline 136
# (default "30"), not an integer. See https://nf-co.re/sarek/3.8.1/parameters/ . - Network accessline 136
# (default "30"), not an integer. See https://nf-co.re/sarek/3.8.1/parameters/ . - Network accessline 403
"""Expand to absolute POSIX path, but pass URI schemes (s3://, http://) through unchanged.""" - Network accessline 403
"""Expand to absolute POSIX path, but pass URI schemes (s3://, http://) through unchanged."""
skills/nfcore-sarek-wrapper/pipeline_source.py
skills/nfcore-sarek-wrapper/preflight.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 207
"""Local-first by default: reject remote samplesheet inputs and user-supplied reference paths (s3://, gs://, https://, ftp://, …) unless allow_remote_inputs - Network accessline 207
"""Local-first by default: reject remote samplesheet inputs and user-supplied reference paths (s3://, gs://, https://, ftp://, …) unless allow_remote_inputs - Network accessline 208
reference paths (s3://, gs://, https://, ftp://, …) unless allow_remote_inputs - Network accessline 208
reference paths (s3://, gs://, https://, ftp://, …) unless allow_remote_inputs - Access to secretsline 708
[Credential-related source omitted] - Access to secretsline 708
[Credential-related source omitted] - Access to secretsline 709
[Credential-related source omitted] - Access to secretsline 709
[Credential-related source omitted] - Network accessline 910
fix=( "Use --demo (which runs -profile test with the correct mirror), or pass " "--igenomes-base https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ " - Network accessline 910
fix=( "Use --demo (which runs -profile test with the correct mirror), or pass " "--igenomes-base https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ " - Network accessline 911
"Use --demo (which runs -profile test with the correct mirror), or pass " "--igenomes-base https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ " "to match conf/test.config. For a real analys - Network accessline 911
"Use --demo (which runs -profile test with the correct mirror), or pass " "--igenomes-base https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ " "to match conf/test.config. For a real analys - Network accessline 912
"--igenomes-base https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ " - Network accessline 912
"--igenomes-base https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/ " - Access to secretsline 1580
[Credential-related source omitted] - Access to secretsline 1580
[Credential-related source omitted] - Access to secretsline 1596
[Credential-related source omitted] - Access to secretsline 1596
[Credential-related source omitted]
skills/nfcore-sarek-wrapper/provenance.py
skills/nfcore-sarek-wrapper/remap_paths.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 5
Local samplesheet input paths (fastq_1, fastq_2, spring_1, spring_2, bam, bai, cram, crai, vcf, table) are stored as absolute paths (required by Nextflow); remote data URLs (s3://, https://, ...) are passed through unchanged and need no - Network accessline 5
Local samplesheet input paths (fastq_1, fastq_2, spring_1, spring_2, bam, bai, cram, crai, vcf, table) are stored as absolute paths (required by Nextflow); remote data URLs (s3://, https://, ...) are passed through unchanged and need no - Network accessline 6
cram, crai, vcf, table) are stored as absolute paths (required by Nextflow); remote data URLs (s3://, https://, ...) are passed through unchanged and need no remapping. Reference/index paths are stored in params.yaml, not in commands.sh. - Network accessline 6
cram, crai, vcf, table) are stored as absolute paths (required by Nextflow); remote data URLs (s3://, https://, ...) are passed through unchanged and need no remapping. Reference/index paths are stored in params.yaml, not in commands.sh. - Network accessline 7
remote data URLs (s3://, https://, ...) are passed through unchanged and need no - Network accessline 7
remote data URLs (s3://, https://, ...) are passed through unchanged and need no - Network accessline 27
Remote URIs (s3://, https://, etc.) are recognized and skipped automatically - Network accessline 27
Remote URIs (s3://, https://, etc.) are recognized and skipped automatically - Network accessline 275
For nf-core/sarek the wrapper passes references via -params-file, so this is the function that makes a bundle fully portable. URIs (s3://, https://, …), - Network accessline 275
For nf-core/sarek the wrapper passes references via -params-file, so this is the function that makes a bundle fully portable. URIs (s3://, https://, …), - Network accessline 276
the function that makes a bundle fully portable. URIs (s3://, https://, …), - Network accessline 276
the function that makes a bundle fully portable. URIs (s3://, https://, …), - Network accessline 329
Remote URIs (s3://, https://, etc.) and bash variable references ($VAR/… - Network accessline 329
Remote URIs (s3://, https://, etc.) and bash variable references ($VAR/… - Network accessline 347
Remote URIs (s3://, https://, etc.) and bash variable references are skipped - Network accessline 347
Remote URIs (s3://, https://, etc.) and bash variable references are skipped
skills/nfcore-sarek-wrapper/reporting.py
skills/nfcore-sarek-wrapper/samplesheet_builder.py
skills/nfcore-sarek-wrapper/schemas.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 55
# 25 profiles from nf-core/sarek 3.8.1 nextflow.config (verified against # https://github.com/nf-core/sarek/blob/3.8.1/nextflow.config — profiles block). - Network accessline 55
# 25 profiles from nf-core/sarek 3.8.1 nextflow.config (verified against # https://github.com/nf-core/sarek/blob/3.8.1/nextflow.config — profiles block). - Network accessline 56
# https://github.com/nf-core/sarek/blob/3.8.1/nextflow.config — profiles block). - Network accessline 56
# https://github.com/nf-core/sarek/blob/3.8.1/nextflow.config — profiles block). - Network accessline 148
# The 42 iGenomes keys accepted by --genome, mirrored from nf-core/sarek 3.8.1 conf/igenomes.config # https://raw.githubusercontent.com/nf-core/sarek/3.8.1/conf/igenomes.config - Network accessline 148
# The 42 iGenomes keys accepted by --genome, mirrored from nf-core/sarek 3.8.1 conf/igenomes.config # https://raw.githubusercontent.com/nf-core/sarek/3.8.1/conf/igenomes.config - Network accessline 149
# https://raw.githubusercontent.com/nf-core/sarek/3.8.1/conf/igenomes.config - Network accessline 149
# https://raw.githubusercontent.com/nf-core/sarek/3.8.1/conf/igenomes.config
skills/nfcore-sarek-wrapper/tests/conftest.py
skills/nfcore-sarek-wrapper/tests/preflight_fixtures.py
skills/nfcore-sarek-wrapper/tests/test_catalog_consistency.py
skills/nfcore-sarek-wrapper/tests/test_cli_direct_invocation.py
skills/nfcore-sarek-wrapper/tests/test_current_audit_regressions.py
skills/nfcore-sarek-wrapper/tests/test_executor.py
skills/nfcore-sarek-wrapper/tests/test_nfcore_sarek_wrapper.py
skills/nfcore-sarek-wrapper/tests/test_outputs_parser.py
skills/nfcore-sarek-wrapper/tests/test_params_builder.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 159
"""A remote --multiqc-config / --multiqc-logo URI must be written to params.yaml verbatim, not resolved as a local path (which collapses the scheme, e.g. https://host/x -> <cwd>/https:/host/x). Parity with the genome - Network accessline 159
"""A remote --multiqc-config / --multiqc-logo URI must be written to params.yaml verbatim, not resolved as a local path (which collapses the scheme, e.g. https://host/x -> <cwd>/https:/host/x). Parity with the genome - Network accessline 160
params.yaml verbatim, not resolved as a local path (which collapses the scheme, e.g. https://host/x -> <cwd>/https:/host/x). Parity with the genome reference fields, which already pass URIs through.""" - Network accessline 160
params.yaml verbatim, not resolved as a local path (which collapses the scheme, e.g. https://host/x -> <cwd>/https:/host/x). Parity with the genome reference fields, which already pass URIs through.""" - Network accessline 161
scheme, e.g. https://host/x -> <cwd>/https:/host/x). Parity with the genome - Network accessline 161
scheme, e.g. https://host/x -> <cwd>/https:/host/x). Parity with the genome - Network accessline 163
uri = "https://raw.githubusercontent.com/nf-core/sarek/3.8.1/assets/multiqc_config.yml" - Network accessline 163
uri = "https://raw.githubusercontent.com/nf-core/sarek/3.8.1/assets/multiqc_config.yml"
skills/nfcore-sarek-wrapper/tests/test_portability_remap_interpreter.py
skills/nfcore-sarek-wrapper/tests/test_preflight.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 1146
def test_testdata_genome_accepted_with_test_datasets_igenomes_base(): base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" - Network accessline 1146
def test_testdata_genome_accepted_with_test_datasets_igenomes_base(): base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" - Network accessline 1147
base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" - Network accessline 1147
base = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/" - Network accessline 1358
with pytest.raises(SkillError) as exc: _pf._check_remote_inputs( {"fasta": "https://example.org/genome.fa"}, {}, allow_remote_inputs=False - Network accessline 1358
with pytest.raises(SkillError) as exc: _pf._check_remote_inputs( {"fasta": "https://example.org/genome.fa"}, {}, allow_remote_inputs=False - Network accessline 1359
_pf._check_remote_inputs( {"fasta": "https://example.org/genome.fa"}, {}, allow_remote_inputs=False ) - Network accessline 1359
_pf._check_remote_inputs( {"fasta": "https://example.org/genome.fa"}, {}, allow_remote_inputs=False ) - Network accessline 1360
{"fasta": "https://example.org/genome.fa"}, {}, allow_remote_inputs=False - Network accessline 1360
{"fasta": "https://example.org/genome.fa"}, {}, allow_remote_inputs=False
skills/nfcore-sarek-wrapper/tests/test_provenance.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 54
source_kind: str = "remote_repo" resolved_version: str = "3.8.1" resolved_uri: str = "https://github.com/nf-core/sarek" - Network accessline 54
source_kind: str = "remote_repo" resolved_version: str = "3.8.1" resolved_uri: str = "https://github.com/nf-core/sarek" - Network accessline 55
resolved_version: str = "3.8.1" resolved_uri: str = "https://github.com/nf-core/sarek" local_path: str | None = None - Network accessline 55
resolved_version: str = "3.8.1" resolved_uri: str = "https://github.com/nf-core/sarek" local_path: str | None = None - Network accessline 56
resolved_uri: str = "https://github.com/nf-core/sarek" - Network accessline 56
resolved_uri: str = "https://github.com/nf-core/sarek" - Network accessline 164
def test_reference_checksums_uri_passthrough(): params = {"fasta": "s3://bucket/hg38.fa", "dbsnp": "https://example.com/dbsnp.vcf.gz"} - Network accessline 164
def test_reference_checksums_uri_passthrough(): params = {"fasta": "s3://bucket/hg38.fa", "dbsnp": "https://example.com/dbsnp.vcf.gz"} - Network accessline 165
params = {"fasta": "s3://bucket/hg38.fa", "dbsnp": "https://example.com/dbsnp.vcf.gz"} - Network accessline 165
params = {"fasta": "s3://bucket/hg38.fa", "dbsnp": "https://example.com/dbsnp.vcf.gz"} - Network accessline 166
out = compute_reference_checksums(params) assert out["fasta"] == "s3://bucket/hg38.fa" assert out["dbsnp"] == "https://example.com/dbsnp.vcf.gz" - Network accessline 166
out = compute_reference_checksums(params) assert out["fasta"] == "s3://bucket/hg38.fa" assert out["dbsnp"] == "https://example.com/dbsnp.vcf.gz" - Network accessline 168
assert out["dbsnp"] == "https://example.com/dbsnp.vcf.gz" - Network accessline 168
assert out["dbsnp"] == "https://example.com/dbsnp.vcf.gz"
skills/nfcore-sarek-wrapper/tests/test_remap_paths.py
skills/nfcore-sarek-wrapper/tests/test_reporting.py
skills/nfcore-sarek-wrapper/tests/test_samplesheet_builder.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 64
def test_samplesheet_allows_url_inputs_without_local_exists(tmp_path): input_path = tmp_path / "remote.csv" _write_delimited(input_path, [_row(tmp_path, fastq_1="https://example.org/S1_R1.fastq.gz")], ",") - Network accessline 64
def test_samplesheet_allows_url_inputs_without_local_exists(tmp_path): input_path = tmp_path / "remote.csv" _write_delimited(input_path, [_row(tmp_path, fastq_1="https://example.org/S1_R1.fastq.gz")], ",") - Network accessline 66
_write_delimited(input_path, [_row(tmp_path, fastq_1="https://example.org/S1_R1.fastq.gz")], ",") - Network accessline 66
_write_delimited(input_path, [_row(tmp_path, fastq_1="https://example.org/S1_R1.fastq.gz")], ",") - Network accessline 70
assert "https://example.org/S1_R1.fastq.gz" in report["fastq_paths"] - Network accessline 70
assert "https://example.org/S1_R1.fastq.gz" in report["fastq_paths"] - Network accessline 116
_write_delimited( input_path, [_row(tmp_path, sex="NA", status="1", fastq_1="https://example.org/T1_R1.fastq.gz")], - Network accessline 116
_write_delimited( input_path, [_row(tmp_path, sex="NA", status="1", fastq_1="https://example.org/T1_R1.fastq.gz")], - Network accessline 117
input_path, [_row(tmp_path, sex="NA", status="1", fastq_1="https://example.org/T1_R1.fastq.gz")], ",", - Network accessline 117
input_path, [_row(tmp_path, sex="NA", status="1", fastq_1="https://example.org/T1_R1.fastq.gz")], ",", - Network accessline 118
[_row(tmp_path, sex="NA", status="1", fastq_1="https://example.org/T1_R1.fastq.gz")], - Network accessline 118
[_row(tmp_path, sex="NA", status="1", fastq_1="https://example.org/T1_R1.fastq.gz")],
skills/nfcore-scrnaseq-wrapper/CHANGELOG.md
- Network accessline 3
All notable changes to the `nfcore-scrnaseq-wrapper` ClawBio skill are documented here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 3
All notable changes to the `nfcore-scrnaseq-wrapper` ClawBio skill are documented here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 4
here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 4
here. The format roughly follows [Keep a Changelog](https://keepachangelog.com) - Network accessline 229
- **Remote reference URIs are no longer corrupted in `params.yaml`.** With `--allow-remote-inputs`, a remote `--fasta`/`--gtf`/`--transcript-fasta`/index URI (`https://`, `s3://`, `gs://`, `ftp://`, …) was resolved as a local path by - Network accessline 229
- **Remote reference URIs are no longer corrupted in `params.yaml`.** With `--allow-remote-inputs`, a remote `--fasta`/`--gtf`/`--transcript-fasta`/index URI (`https://`, `s3://`, `gs://`, `ftp://`, …) was resolved as a local path by - Network accessline 230
`--allow-remote-inputs`, a remote `--fasta`/`--gtf`/`--transcript-fasta`/index URI (`https://`, `s3://`, `gs://`, `ftp://`, …) was resolved as a local path by `params_builder`, collapsing the scheme and anchoring it to the working - Network accessline 230
`--allow-remote-inputs`, a remote `--fasta`/`--gtf`/`--transcript-fasta`/index URI (`https://`, `s3://`, `gs://`, `ftp://`, …) was resolved as a local path by `params_builder`, collapsing the scheme and anchoring it to the working - Network accessline 231
URI (`https://`, `s3://`, `gs://`, `ftp://`, …) was resolved as a local path by - Network accessline 231
URI (`https://`, `s3://`, `gs://`, `ftp://`, …) was resolved as a local path by - Network accessline 232
`params_builder`, collapsing the scheme and anchoring it to the working directory (`https://host/x` → `<cwd>/https:/host/x`), which nf-core then rejected during parameter validation. Reference fields now preserve URIs verbatim (via a - Network accessline 232
`params_builder`, collapsing the scheme and anchoring it to the working directory (`https://host/x` → `<cwd>/https:/host/x`), which nf-core then rejected during parameter validation. Reference fields now preserve URIs verbatim (via a - Network accessline 233
directory (`https://host/x` → `<cwd>/https:/host/x`), which nf-core then rejected - Network accessline 233
directory (`https://host/x` → `<cwd>/https:/host/x`), which nf-core then rejected - Network accessline 293
(local-first by default).** Samplesheet FASTQs and reference/index paths must be local unless the flag is passed; otherwise preflight rejects remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) with `REMOTE_INPUT_NOT_ALLOWED`, so - Network accessline 293
(local-first by default).** Samplesheet FASTQs and reference/index paths must be local unless the flag is passed; otherwise preflight rejects remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) with `REMOTE_INPUT_NOT_ALLOWED`, so - Network accessline 294
be local unless the flag is passed; otherwise preflight rejects remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) with `REMOTE_INPUT_NOT_ALLOWED`, so the "keeps processing local / prevents accidental cloud access" guarantee is - Network accessline 294
be local unless the flag is passed; otherwise preflight rejects remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) with `REMOTE_INPUT_NOT_ALLOWED`, so the "keeps processing local / prevents accidental cloud access" guarantee is - Network accessline 295
(`s3://`, `gs://`, `https://`, `ftp://`, …) with `REMOTE_INPUT_NOT_ALLOWED`, so - Network accessline 295
(`s3://`, `gs://`, `https://`, `ftp://`, …) with `REMOTE_INPUT_NOT_ALLOWED`, so
skills/nfcore-scrnaseq-wrapper/README.md
- Network accessline 53
**Local-first by default.** Samplesheet FASTQs and reference/index inputs must be local paths; remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) are rejected at preflight (`REMOTE_INPUT_NOT_ALLOWED`) so genetic data and references sta - Network accessline 53
**Local-first by default.** Samplesheet FASTQs and reference/index inputs must be local paths; remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) are rejected at preflight (`REMOTE_INPUT_NOT_ALLOWED`) so genetic data and references sta
skills/nfcore-scrnaseq-wrapper/SKILL.md
- Network accessline 29
always: false emoji: 🧫 homepage: https://github.com/ClawBio/ClawBio - Network accessline 29
always: false emoji: 🧫 homepage: https://github.com/ClawBio/ClawBio - Network accessline 30
emoji: 🧫 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 30
emoji: 🧫 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 31
homepage: https://github.com/ClawBio/ClawBio - Network accessline 31
homepage: https://github.com/ClawBio/ClawBio - Network accessline 178
**Local-first by default.** Samplesheet FASTQs and reference/index inputs must be local paths unless you explicitly opt in. Remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) are **rejected** at preflight with `REMOTE_INPUT_NOT_ALLOWED - Network accessline 178
**Local-first by default.** Samplesheet FASTQs and reference/index inputs must be local paths unless you explicitly opt in. Remote URIs (`s3://`, `gs://`, `https://`, `ftp://`, …) are **rejected** at preflight with `REMOTE_INPUT_NOT_ALLOWED - Network accessline 267
| `--protocol` | string | `None` | Chemistry/protocol forwarded to the aligner. Required for `standard`, `star`, and `kallisto`; omitted only preserves CellRanger auto-detection for `cellranger`, `cellrangerarc`, and `cellrangermulti`. Expl - Network accessline 267
| `--protocol` | string | `None` | Chemistry/protocol forwarded to the aligner. Required for `standard`, `star`, and `kallisto`; omitted only preserves CellRanger auto-detection for `cellranger`, `cellrangerarc`, and `cellrangermulti`. Expl - Network accessline 268
| `--genome` | string | — | iGenomes shortcut (`GRCh38`, `mm10`, etc.) — mutually exclusive with `--fasta`/`--gtf` and all index flags | | `--igenomes-base` | string | — | Base URL or local path for iGenomes (default `s3://ngi-igenomes/igen - Network accessline 268
| `--genome` | string | — | iGenomes shortcut (`GRCh38`, `mm10`, etc.) — mutually exclusive with `--fasta`/`--gtf` and all index flags | | `--igenomes-base` | string | — | Base URL or local path for iGenomes (default `s3://ngi-igenomes/igen - Network accessline 269
| `--igenomes-base` | string | — | Base URL or local path for iGenomes (default `s3://ngi-igenomes/igenomes/`). Use for local mirrors or air-gapped clusters. A **local** base path is existence-checked in preflight when `--genome` is set (re - Network accessline 269
| `--igenomes-base` | string | — | Base URL or local path for iGenomes (default `s3://ngi-igenomes/igenomes/`). Use for local mirrors or air-gapped clusters. A **local** base path is existence-checked in preflight when `--genome` is set (re - Network accessline 493
- [nf-core/scrnaseq 4.1.0](https://nf-co.re/scrnaseq/4.1.0) - Network accessline 493
- [nf-core/scrnaseq 4.1.0](https://nf-co.re/scrnaseq/4.1.0) - Network accessline 494
- [nf-core/scrnaseq usage](https://nf-co.re/scrnaseq/4.1.0/docs/usage/) - Network accessline 494
- [nf-core/scrnaseq usage](https://nf-co.re/scrnaseq/4.1.0/docs/usage/) - Network accessline 495
- [nf-core/scrnaseq parameters](https://nf-co.re/scrnaseq/4.1.0/parameters/) - Network accessline 495
- [nf-core/scrnaseq parameters](https://nf-co.re/scrnaseq/4.1.0/parameters/) - Network accessline 496
- [nf-core/scrnaseq output](https://nf-co.re/scrnaseq/4.1.0/docs/output/) - Network accessline 496
- [nf-core/scrnaseq output](https://nf-co.re/scrnaseq/4.1.0/docs/output/) - Network accessline 497
- [Nextflow](https://www.nextflow.io/) - Network accessline 497
- [Nextflow](https://www.nextflow.io/) - Network accessline 498
- [Alevin-fry / Simpleaf](https://simpleaf.readthedocs.io/) - Network accessline 498
- [Alevin-fry / Simpleaf](https://simpleaf.readthedocs.io/) - Network accessline 499
- [STARsolo](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md) - Network accessline 499
- [STARsolo](https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md) - Network accessline 500
- [kb-python / BUStools](https://www.kallistobus.tools/) - Network accessline 500
- [kb-python / BUStools](https://www.kallistobus.tools/)
skills/nfcore-scrnaseq-wrapper/_isolated_imports.py
skills/nfcore-scrnaseq-wrapper/command_builder.py
skills/nfcore-scrnaseq-wrapper/errors.py
skills/nfcore-scrnaseq-wrapper/executor.py
skills/nfcore-scrnaseq-wrapper/nfcore_4_1_0_contract.py
- Executable scriptline 1
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"custom_config_base": { "type": "string", "default": "https://raw.githubusercontent.com/nf-core/configs/master", - Network accessline 131
"custom_config_base": { "type": "string", "default": "https://raw.githubusercontent.com/nf-core/configs/master", - Network accessline 132
"type": "string", "default": "https://raw.githubusercontent.com/nf-core/configs/master", }, - Network accessline 132
"type": "string", "default": "https://raw.githubusercontent.com/nf-core/configs/master", }, - Network accessline 133
"default": "https://raw.githubusercontent.com/nf-core/configs/master", - Network accessline 133
"default": "https://raw.githubusercontent.com/nf-core/configs/master", - Network accessline 161
"pipelines_testdata_base_path": { "type": "string", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", - Network accessline 161
"pipelines_testdata_base_path": { "type": "string", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", - Network accessline 162
"type": "string", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", }, - Network accessline 162
"type": "string", "default": "https://raw.githubusercontent.com/nf-core/test-datasets/", }, - Network accessline 163
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/", - Network accessline 163
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/", - Network accessline 270
# ── Protocol routing matrix — faithful mirror of assets/protocols.json @ 4.1.0 ─ # Source of truth (verbatim semantics): # https://github.com/nf-core/scrnaseq/4.1.0/assets/protocols.json - Network accessline 270
# ── Protocol routing matrix — faithful mirror of assets/protocols.json @ 4.1.0 ─ # Source of truth (verbatim semantics): # https://github.com/nf-core/scrnaseq/4.1.0/assets/protocols.json - Network accessline 271
# Source of truth (verbatim semantics): # https://github.com/nf-core/scrnaseq/4.1.0/assets/protocols.json # Keys are wrapper *presets* (standard == simpleaf); values are the protocol - Network accessline 271
# Source of truth (verbatim semantics): # https://github.com/nf-core/scrnaseq/4.1.0/assets/protocols.json # Keys are wrapper *presets* (standard == simpleaf); values are the protocol - Network accessline 272
# https://github.com/nf-core/scrnaseq/4.1.0/assets/protocols.json - Network accessline 272
# https://github.com/nf-core/scrnaseq/4.1.0/assets/protocols.json
skills/nfcore-scrnaseq-wrapper/nfcore_scrnaseq_wrapper.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 314
help=( "Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 314
help=( "Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 315
"Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " "genetic data and references stay on the local machine. When enab - Network accessline 315
"Opt in to remote samplesheet inputs and reference paths (s3://, gs://, " "https://, ftp://, …). Default is local-first: remote URIs are rejected so " "genetic data and references stay on the local machine. When enab - Network accessline 316
"https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 316
"https://, ftp://, …). Default is local-first: remote URIs are rejected so " - Network accessline 1086
nf-core's guidance is that ``resourceLimits`` should match the machine's maximum (https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1086
nf-core's guidance is that ``resourceLimits`` should match the machine's maximum (https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1087
(https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1087
(https://nf-co.re/docs/running/configuration/nextflow-for-your-system). Native - Network accessline 1118
"// does not abort real runs whose production requirements exceed this machine.\n" "// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-f - Network accessline 1118
"// does not abort real runs whose production requirements exceed this machine.\n" "// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-f - Network accessline 1119
"// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" "process {\n" - Network accessline 1119
"// Follows nf-core resourceLimits guidance (values match the machine maximum):\n" "// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" "process {\n" - Network accessline 1120
"// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" - Network accessline 1120
"// https://nf-co.re/docs/running/configuration/nextflow-for-your-system\n" - Access to secretsline 1245
[Credential-related source omitted] - Access to secretsline 1245
[Credential-related source omitted] - Access to secretsline 1296
[Credential-related source omitted] - Access to secretsline 1296
[Credential-related source omitted]
skills/nfcore-scrnaseq-wrapper/outputs_parser.py
skills/nfcore-scrnaseq-wrapper/params_builder.py
- Executable scriptline 1
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"""Like :func:`_posix`, but pass remote URIs (``s3://``, ``gs://``, ``https://``, - Network accessline 52
"""Like :func:`_posix`, but pass remote URIs (``s3://``, ``gs://``, ``https://``, - Network accessline 55
``Path(...).resolve()`` on a URI corrupts it: the ``//`` collapses and the scheme is anchored to the current directory (``https://host/x`` → ``<cwd>/https:/host/x``), which nf-core then rejects at - Network accessline 55
``Path(...).resolve()`` on a URI corrupts it: the ``//`` collapses and the scheme is anchored to the current directory (``https://host/x`` → ``<cwd>/https:/host/x``), which nf-core then rejects at - Network accessline 56
scheme is anchored to the current directory (``https://host/x`` → ``<cwd>/https:/host/x``), which nf-core then rejects at parameter validation. Remote references are gated behind ``--allow-remote-inputs`` - Network accessline 56
scheme is anchored to the current directory (``https://host/x`` → ``<cwd>/https:/host/x``), which nf-core then rejects at parameter validation. Remote references are gated behind ``--allow-remote-inputs`` - Network accessline 57
(``https://host/x`` → ``<cwd>/https:/host/x``), which nf-core then rejects at - Network accessline 57
(``https://host/x`` → ``<cwd>/https:/host/x``), which nf-core then rejects at
skills/nfcore-scrnaseq-wrapper/pipeline_source.py
skills/nfcore-scrnaseq-wrapper/preflight.py
- Executable scriptline 1
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"""Local-first by default: reject remote input/reference URIs (s3://, gs://, https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in which case - Network accessline 477
"""Local-first by default: reject remote input/reference URIs (s3://, gs://, https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in which case - Network accessline 478
https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in which case - Network accessline 478
https://, ftp://, …) unless ``--allow-remote-inputs`` is set, in which case - Network accessline 610
# Remote URI (s3://, gs://, https://, …): Nextflow resolves it at runtime, - Network accessline 610
# Remote URI (s3://, gs://, https://, …): Nextflow resolves it at runtime, - Access to secretsline 821
[Credential-related source omitted] - Access to secretsline 821
[Credential-related source omitted] - Access to secretsline 837
[Credential-related source omitted] - Access to secretsline 837
[Credential-related source omitted] - Network accessline 1351
Remote bases (s3://, https://, ...) are resolved by Nextflow at runtime and - Network accessline 1351
Remote bases (s3://, https://, ...) are resolved by Nextflow at runtime and - Network accessline 1361
return if "://" in str(base): return # remote base resolved by Nextflow (s3://, https://, gs://, ...) - Network accessline 1361
return if "://" in str(base): return # remote base resolved by Nextflow (s3://, https://, gs://, ...) - Network accessline 1362
if "://" in str(base): return # remote base resolved by Nextflow (s3://, https://, gs://, ...) base_path = Path(str(base)).expanduser() - Network accessline 1362
if "://" in str(base): return # remote base resolved by Nextflow (s3://, https://, gs://, ...) base_path = Path(str(base)).expanduser() - Network accessline 1363
return # remote base resolved by Nextflow (s3://, https://, gs://, ...) - Network accessline 1363
return # remote base resolved by Nextflow (s3://, https://, gs://, ...)
skills/nfcore-scrnaseq-wrapper/provenance.py
- Executable scriptline 1
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# fastq_paths and reference_paths are deliberately kept absolute: they point # to external data outside the bundle and are remapped by remap_paths.py on # replay, not relativised against the output dir. Remote URIs (s3://, h - Network accessline 216
# fastq_paths and reference_paths are deliberately kept absolute: they point # to external data outside the bundle and are remapped by remap_paths.py on # replay, not relativised against the output dir. Remote URIs (s3://, h - Network accessline 217
# to external data outside the bundle and are remapped by remap_paths.py on # replay, not relativised against the output dir. Remote URIs (s3://, https://, # …) are preserved verbatim — Path().as_posix() would collapse the ` - Network accessline 217
# to external data outside the bundle and are remapped by remap_paths.py on # replay, not relativised against the output dir. Remote URIs (s3://, https://, # …) are preserved verbatim — Path().as_posix() would collapse the ` - Network accessline 218
# replay, not relativised against the output dir. Remote URIs (s3://, https://, - Network accessline 218
# replay, not relativised against the output dir. Remote URIs (s3://, https://,
skills/nfcore-scrnaseq-wrapper/remap_paths.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 23
Preview any change without modifying files by adding --dry-run. Remote URIs (s3://, https://, ...) and $VAR references are always skipped. - Network accessline 23
Preview any change without modifying files by adding --dry-run. Remote URIs (s3://, https://, ...) and $VAR references are always skipped. - Network accessline 24
Remote URIs (s3://, https://, ...) and $VAR references are always skipped. - Network accessline 24
Remote URIs (s3://, https://, ...) and $VAR references are always skipped. - Network accessline 158
Remote URIs (s3://, https://, ...) and $VAR references are skipped. - Network accessline 158
Remote URIs (s3://, https://, ...) and $VAR references are skipped.
skills/nfcore-scrnaseq-wrapper/reporting.py
skills/nfcore-scrnaseq-wrapper/repro_commands.py
skills/nfcore-scrnaseq-wrapper/samplesheet_builder.py
- Executable scriptline 1
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# A resolved FASTQ value is either a normalized local Path or a remote URI kept # verbatim as a str (s3://, gs://, https://, …). nf-core/scrnaseq supports remote - Network accessline 45
# A resolved FASTQ value is either a normalized local Path or a remote URI kept # verbatim as a str (s3://, gs://, https://, …). nf-core/scrnaseq supports remote - Network accessline 46
# verbatim as a str (s3://, gs://, https://, …). nf-core/scrnaseq supports remote - Network accessline 46
# verbatim as a str (s3://, gs://, https://, …). nf-core/scrnaseq supports remote - Network accessline 516
# Remote URIs (s3://, gs://, https://, …) are passed through verbatim: nf-core - Network accessline 516
# Remote URIs (s3://, gs://, https://, …) are passed through verbatim: nf-core
skills/nfcore-scrnaseq-wrapper/schemas.py
skills/nfcore-scrnaseq-wrapper/tests/conftest.py
skills/nfcore-scrnaseq-wrapper/tests/test_audit_fixes.py
skills/nfcore-scrnaseq-wrapper/tests/test_audit_round2.py
skills/nfcore-scrnaseq-wrapper/tests/test_audit_round3.py
skills/nfcore-scrnaseq-wrapper/tests/test_audit_round4.py
skills/nfcore-scrnaseq-wrapper/tests/test_audit_round5.py
skills/nfcore-scrnaseq-wrapper/tests/test_bundle_portability.py
skills/nfcore-scrnaseq-wrapper/tests/test_cli_direct_invocation.py
skills/nfcore-scrnaseq-wrapper/tests/test_command_builder.py
skills/nfcore-scrnaseq-wrapper/tests/test_contract_generator.py
skills/nfcore-scrnaseq-wrapper/tests/test_error_codes.py
skills/nfcore-scrnaseq-wrapper/tests/test_executor.py
skills/nfcore-scrnaseq-wrapper/tests/test_nfcore_contract.py
- Executable scriptline 1
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# ── Protocol matrix: faithful mirror of assets/protocols.json @ 4.1.0 ───────── # Source of truth: # https://github.com/nf-core/scrnaseq/blob/4.1.0/assets/protocols.json - Network accessline 74
# ── Protocol matrix: faithful mirror of assets/protocols.json @ 4.1.0 ───────── # Source of truth: # https://github.com/nf-core/scrnaseq/blob/4.1.0/assets/protocols.json - Network accessline 75
# Source of truth: # https://github.com/nf-core/scrnaseq/blob/4.1.0/assets/protocols.json # These tests freeze the upstream truth so the preflight protocol rules can never - Network accessline 75
# Source of truth: # https://github.com/nf-core/scrnaseq/blob/4.1.0/assets/protocols.json # These tests freeze the upstream truth so the preflight protocol rules can never - Network accessline 76
# https://github.com/nf-core/scrnaseq/blob/4.1.0/assets/protocols.json - Network accessline 76
# https://github.com/nf-core/scrnaseq/blob/4.1.0/assets/protocols.json
skills/nfcore-scrnaseq-wrapper/tests/test_nfcore_scrnaseq_wrapper.py
skills/nfcore-scrnaseq-wrapper/tests/test_outputs_parser.py
skills/nfcore-scrnaseq-wrapper/tests/test_params_builder.py
- Executable scriptline 1
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"""Remote reference URIs (staged by Nextflow when --allow-remote-inputs is set) must be written to params.yaml verbatim. Resolving them as local paths corrupts the scheme (https://host/... -> <cwd>/https:/host/...), which nf-core - Network accessline 361
"""Remote reference URIs (staged by Nextflow when --allow-remote-inputs is set) must be written to params.yaml verbatim. Resolving them as local paths corrupts the scheme (https://host/... -> <cwd>/https:/host/...), which nf-core - Network accessline 362
must be written to params.yaml verbatim. Resolving them as local paths corrupts the scheme (https://host/... -> <cwd>/https:/host/...), which nf-core then rejects during parameter validation.""" - Network accessline 362
must be written to params.yaml verbatim. Resolving them as local paths corrupts the scheme (https://host/... -> <cwd>/https:/host/...), which nf-core then rejects during parameter validation.""" - Network accessline 363
corrupts the scheme (https://host/... -> <cwd>/https:/host/...), which nf-core - Network accessline 363
corrupts the scheme (https://host/... -> <cwd>/https:/host/...), which nf-core - Network accessline 366
samplesheet.parent.mkdir(parents=True) samplesheet.write_text("sample,fastq_1,fastq_2\n", encoding="utf-8") fasta_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa" - Network accessline 366
samplesheet.parent.mkdir(parents=True) samplesheet.write_text("sample,fastq_1,fastq_2\n", encoding="utf-8") fasta_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa" - Network accessline 367
samplesheet.write_text("sample,fastq_1,fastq_2\n", encoding="utf-8") fasta_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa" gtf_uri = "https://github.com/nf-core/test-datasets/raw/scr - Network accessline 367
samplesheet.write_text("sample,fastq_1,fastq_2\n", encoding="utf-8") fasta_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa" gtf_uri = "https://github.com/nf-core/test-datasets/raw/scr - Network accessline 368
fasta_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa" - Network accessline 368
fasta_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa" - Network accessline 369
gtf_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/gencode.vM19.annotation.chr19.gtf" - Network accessline 369
gtf_uri = "https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/gencode.vM19.annotation.chr19.gtf"
skills/nfcore-scrnaseq-wrapper/tests/test_pipeline_source.py
skills/nfcore-scrnaseq-wrapper/tests/test_portability_remap_interpreter.py
skills/nfcore-scrnaseq-wrapper/tests/test_preflight.py
- Executable scriptline 1
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Executable file - Network accessline 82
"""Remote reference URIs (s3://, gs://, https://) are passed through: Nextflow - Network accessline 82
"""Remote reference URIs (s3://, gs://, https://) are passed through: Nextflow - Network accessline 86
{ "fasta": "s3://bucket/genome.fa", "gtf": "https://example.org/genes.gtf", - Network accessline 86
{ "fasta": "s3://bucket/genome.fa", "gtf": "https://example.org/genes.gtf", - Network accessline 87
"fasta": "s3://bucket/genome.fa", "gtf": "https://example.org/genes.gtf", "star_index": "gs://bucket/star/", - Network accessline 87
"fasta": "s3://bucket/genome.fa", "gtf": "https://example.org/genes.gtf", "star_index": "gs://bucket/star/", - Network accessline 88
"gtf": "https://example.org/genes.gtf", - Network accessline 88
"gtf": "https://example.org/genes.gtf", - Network accessline 116
with pytest.raises(SkillError) as exc: preflight._check_remote_inputs( Namespace(allow_remote_inputs=False, fasta="https://example.org/genome.fa"), - Network accessline 116
with pytest.raises(SkillError) as exc: preflight._check_remote_inputs( Namespace(allow_remote_inputs=False, fasta="https://example.org/genome.fa"), - Network accessline 117
preflight._check_remote_inputs( Namespace(allow_remote_inputs=False, fasta="https://example.org/genome.fa"), {"fastq_paths": []}, - Network accessline 117
preflight._check_remote_inputs( Namespace(allow_remote_inputs=False, fasta="https://example.org/genome.fa"), {"fastq_paths": []}, - Network accessline 118
Namespace(allow_remote_inputs=False, fasta="https://example.org/genome.fa"), - Network accessline 118
Namespace(allow_remote_inputs=False, fasta="https://example.org/genome.fa"),
skills/nfcore-scrnaseq-wrapper/tests/test_provenance.py
skills/nfcore-scrnaseq-wrapper/tests/test_remap_paths.py
- Executable scriptline 1
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f"fasta: {real}\n" "gtf: /does/not/exist.gtf\n" "transcript_fasta: https://example.org/tx.fa\n", - Network accessline 210
f"fasta: {real}\n" "gtf: /does/not/exist.gtf\n" "transcript_fasta: https://example.org/tx.fa\n", - Network accessline 211
"gtf: /does/not/exist.gtf\n" "transcript_fasta: https://example.org/tx.fa\n", encoding="utf-8", - Network accessline 211
"gtf: /does/not/exist.gtf\n" "transcript_fasta: https://example.org/tx.fa\n", encoding="utf-8", - Network accessline 212
"transcript_fasta: https://example.org/tx.fa\n", - Network accessline 212
"transcript_fasta: https://example.org/tx.fa\n", - Dangerous shell operationline 275
exec(compile(copied, "remap_paths_bundle", "exec"), namespace) - Dangerous shell operationline 275
exec(compile(copied, "remap_paths_bundle", "exec"), namespace) - Dangerous shell operationline 307
exec(compile(copied, "remap_paths_bundle", "exec"), namespace) - Dangerous shell operationline 307
exec(compile(copied, "remap_paths_bundle", "exec"), namespace)
skills/nfcore-scrnaseq-wrapper/tests/test_reporting.py
skills/nfcore-scrnaseq-wrapper/tests/test_repro_commands.py
skills/nfcore-scrnaseq-wrapper/tests/test_resume_policy.py
skills/nfcore-scrnaseq-wrapper/tests/test_samplesheet_builder.py
- Executable scriptline 1
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Executable file - Network accessline 52
src.write_text( "sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz\n", - Network accessline 52
src.write_text( "sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz\n", - Network accessline 53
"sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz\n", encoding="utf-8", - Network accessline 53
"sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz\n", encoding="utf-8", - Network accessline 54
"sampleA,https://example.org/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz\n", - Network accessline 54
"sampleA,https://example.org/S1_R1.fastq.gz,s3://bucket/S1_R2.fastq.gz\n", - Network accessline 61
assert "https://example.org/S1_R1.fastq.gz" in summary["fastq_paths"] - Network accessline 61
assert "https://example.org/S1_R1.fastq.gz" in summary["fastq_paths"] - Network accessline 62
assert "s3://bucket/S1_R2.fastq.gz" in summary["fastq_paths"] written = out.read_text(encoding="utf-8") assert "https://example.org/S1_R1.fastq.gz" in written - Network accessline 62
assert "s3://bucket/S1_R2.fastq.gz" in summary["fastq_paths"] written = out.read_text(encoding="utf-8") assert "https://example.org/S1_R1.fastq.gz" in written - Network accessline 63
written = out.read_text(encoding="utf-8") assert "https://example.org/S1_R1.fastq.gz" in written assert "s3://bucket/S1_R2.fastq.gz" in written - Network accessline 63
written = out.read_text(encoding="utf-8") assert "https://example.org/S1_R1.fastq.gz" in written assert "s3://bucket/S1_R2.fastq.gz" in written - Network accessline 64
assert "https://example.org/S1_R1.fastq.gz" in written - Network accessline 64
assert "https://example.org/S1_R1.fastq.gz" in written - Network accessline 71
src.write_text( "sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,https://example.org/notes.txt\n", - Network accessline 71
src.write_text( "sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,https://example.org/notes.txt\n", - Network accessline 72
"sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,https://example.org/notes.txt\n", encoding="utf-8", - Network accessline 72
"sample,fastq_1,fastq_2\n" "sampleA,https://example.org/S1_R1.fastq.gz,https://example.org/notes.txt\n", encoding="utf-8", - Network accessline 73
"sampleA,https://example.org/S1_R1.fastq.gz,https://example.org/notes.txt\n", - Network accessline 73
"sampleA,https://example.org/S1_R1.fastq.gz,https://example.org/notes.txt\n",
skills/nutrigx/SKILL.md
- Network accessline 21
always: false emoji: 🥦 homepage: https://github.com/ClawBio/ClawBio - Network accessline 21
always: false emoji: 🥦 homepage: https://github.com/ClawBio/ClawBio - Network accessline 22
emoji: 🥦 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 22
emoji: 🥦 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 23
homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
homepage: https://github.com/ClawBio/ClawBio - Network accessline 331
The SNP panel (`data/snp_panel.json`) is maintained by the skill author. To suggest additions or corrections, contact David de Lorenzo directly via GitHub ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) or open - Network accessline 331
The SNP panel (`data/snp_panel.json`) is maintained by the skill author. To suggest additions or corrections, contact David de Lorenzo directly via GitHub ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) or open - Network accessline 332
To suggest additions or corrections, contact David de Lorenzo directly via GitHub ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) or open an issue tagging him in the main ClawBio repository. - Network accessline 332
To suggest additions or corrections, contact David de Lorenzo directly via GitHub ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) or open an issue tagging him in the main ClawBio repository. - Network accessline 333
GitHub ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) or open - Network accessline 333
GitHub ([@drdaviddelorenzo](https://github.com/drdaviddelorenzo)) or open
skills/nutrigx/examples/generate_patient.py
skills/nutrigx/extract_genotypes.py
skills/nutrigx/generate_report.py
skills/nutrigx/nutrigx.py
skills/nutrigx/nutrigx_repro_bundle.py
skills/nutrigx/parse_input.py
skills/nutrigx/path_safety.py
skills/nutrigx/score_variants.py
skills/nutrigx/tests/test_ancestry_parser.py
skills/nutrigx/tests/test_genotype_validation.py
skills/nutrigx/tests/test_nutrigx.py
skills/nutrigx/tests/test_palindromic_snps.py
skills/nutrigx/tests/test_repro_bundle.py
skills/nutrigx/tests/test_rs953413_direction.py
skills/omics-target-evidence-mapper/SKILL.md
- Network accessline 17
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 17
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 18
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio
skills/omics-target-evidence-mapper/commands.sh
skills/omics-target-evidence-mapper/omics_target_evidence_mapper.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 50
) -> dict[str, Any] | None: try: response = requests.request(method, url, params=params, json=json_body, timeout=timeout) - Network accessline 50
) -> dict[str, Any] | None: try: response = requests.request(method, url, params=params, json=json_body, timeout=timeout) - Network accessline 51
try: response = requests.request(method, url, params=params, json=json_body, timeout=timeout) response.raise_for_status() - Network accessline 51
try: response = requests.request(method, url, params=params, json=json_body, timeout=timeout) response.raise_for_status() - Network accessline 52
response = requests.request(method, url, params=params, json=json_body, timeout=timeout) - Network accessline 52
response = requests.request(method, url, params=params, json=json_body, timeout=timeout) - Network accessline 60
def fetch_uniprot_summary(gene: str) -> dict[str, Any]: url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 60
def fetch_uniprot_summary(gene: str) -> dict[str, Any]: url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 61
url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 61
url = "https://rest.uniprot.org/uniprotkb/search" - Network accessline 96
def fetch_pubmed_hits(gene: str, disease: str | None, max_papers: int) -> dict[str, Any]: term = gene if not disease else f"{gene} AND {disease}" search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 96
def fetch_pubmed_hits(gene: str, disease: str | None, max_papers: int) -> dict[str, Any]: term = gene if not disease else f"{gene} AND {disease}" search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 97
term = gene if not disease else f"{gene} AND {disease}" search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" search_params = { - Network accessline 97
term = gene if not disease else f"{gene} AND {disease}" search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" search_params = { - Network accessline 98
search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 98
search_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 115
summary_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 115
summary_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi" - Network accessline 145
url = "https://api.platform.opentargets.org/api/v4/graphql" - Network accessline 145
url = "https://api.platform.opentargets.org/api/v4/graphql" - Network accessline 191
def fetch_trials(gene: str, disease: str | None, max_trials: int) -> dict[str, Any]: query = gene if not disease else f"{gene} {disease}" url = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 191
def fetch_trials(gene: str, disease: str | None, max_trials: int) -> dict[str, Any]: query = gene if not disease else f"{gene} {disease}" url = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 192
query = gene if not disease else f"{gene} {disease}" url = "https://clinicaltrials.gov/api/v2/studies" params = { - Network accessline 192
query = gene if not disease else f"{gene} {disease}" url = "https://clinicaltrials.gov/api/v2/studies" params = { - Network accessline 193
url = "https://clinicaltrials.gov/api/v2/studies" - Network accessline 193
url = "https://clinicaltrials.gov/api/v2/studies"
skills/omics-target-evidence-mapper/tests/test_omics_target_evidence_mapper.py
skills/omics-target-evidence-mapper/tests/test_omics_unavailable.py
skills/omics-target-evidence-mapper/tests/test_smoke.py
skills/organ-aging-studio/SKILL.md
- Network accessline 55
always: false emoji: "🕰<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio - Network accessline 55
always: false emoji: "🕰<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio - Network accessline 56
emoji: "🕰<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 56
emoji: "🕰<U+FE0F>" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 57
homepage: https://github.com/ClawBio/ClawBio - Network accessline 57
homepage: https://github.com/ClawBio/ClawBio - Network accessline 105
Built on the same pinned [organAging](https://github.com/ludgergoeminne/organAging) coefficients as `proteomics-clock`. **No invented weights.** - Network accessline 105
Built on the same pinned [organAging](https://github.com/ludgergoeminne/organAging) coefficients as `proteomics-clock`. **No invented weights.** - Network accessline 247
Goeminne LJE et al. (2025). *Cell Metabolism* 37(1):205-222.e6. DOI: [10.1016/j.cmet.2024.10.005](https://doi.org/10.1016/j.cmet.2024.10.005) - Network accessline 247
Goeminne LJE et al. (2025). *Cell Metabolism* 37(1):205-222.e6. DOI: [10.1016/j.cmet.2024.10.005](https://doi.org/10.1016/j.cmet.2024.10.005)
skills/organ-aging-studio/data/PROVENANCE.md
- Network accessline 29
- **Use case**: Real Olink NPX for Goeminne organ clocks (longitudinal Day 0/3/7) - **Download**: [Mendeley Data — nf853r8xsj](https://doi.org/10.17632/nf853r8xsj.2) (3 Excel files) - Network accessline 29
- **Use case**: Real Olink NPX for Goeminne organ clocks (longitudinal Day 0/3/7) - **Download**: [Mendeley Data — nf853r8xsj](https://doi.org/10.17632/nf853r8xsj.2) (3 Excel files) - Network accessline 30
- **Download**: [Mendeley Data — nf853r8xsj](https://doi.org/10.17632/nf853r8xsj.2) (3 Excel files) - Network accessline 30
- **Download**: [Mendeley Data — nf853r8xsj](https://doi.org/10.17632/nf853r8xsj.2) (3 Excel files) - Network accessline 36
- **Use case**: Show DNAm clocks correlate with age (r ≈ 0.9) on blood — **not** an input to this skill - **Download** (pick one): - Supplemental beta chunks (~316 MB each): [GSE40279 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi - Network accessline 36
- **Use case**: Show DNAm clocks correlate with age (r ≈ 0.9) on blood — **not** an input to this skill - **Download** (pick one): - Supplemental beta chunks (~316 MB each): [GSE40279 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi - Network accessline 37
- **Download** (pick one): - Supplemental beta chunks (~316 MB each): [GSE40279 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279) → *Supplementary file* - Full average beta: `GSE40279_average_beta.txt.gz` (~1.2 GB) - Network accessline 37
- **Download** (pick one): - Supplemental beta chunks (~316 MB each): [GSE40279 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279) → *Supplementary file* - Full average beta: `GSE40279_average_beta.txt.gz` (~1.2 GB) - Network accessline 38
- Supplemental beta chunks (~316 MB each): [GSE40279 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279) → *Supplementary file* - Network accessline 38
- Supplemental beta chunks (~316 MB each): [GSE40279 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40279) → *Supplementary file* - Network accessline 45
- **Use case**: Future paired proteomic + epigenetic age on the **same** individuals - **Download**: [GSE259312 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE259312) - Network accessline 45
- **Use case**: Future paired proteomic + epigenetic age on the **same** individuals - **Download**: [GSE259312 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE259312) - Network accessline 46
- **Download**: [GSE259312 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE259312) - Network accessline 46
- **Download**: [GSE259312 on GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE259312)
skills/organ-aging-studio/organ_aging_studio.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 297
"```", "", "Coefficients are downloaded from the pinned [organAging](https://github.com/ludgergoeminne/organAging) repository.", - Network accessline 297
"```", "", "Coefficients are downloaded from the pinned [organAging](https://github.com/ludgergoeminne/organAging) repository.", - Network accessline 298
"", "Coefficients are downloaded from the pinned [organAging](https://github.com/ludgergoeminne/organAging) repository.", "Delta values are the raw predicted-minus-chronological gap, not age-residualised acceleration - Network accessline 298
"", "Coefficients are downloaded from the pinned [organAging](https://github.com/ludgergoeminne/organAging) repository.", "Delta values are the raw predicted-minus-chronological gap, not age-residualised acceleration - Network accessline 299
"Coefficients are downloaded from the pinned [organAging](https://github.com/ludgergoeminne/organAging) repository.", - Network accessline 299
"Coefficients are downloaded from the pinned [organAging](https://github.com/ludgergoeminne/organAging) repository.",
skills/organ-aging-studio/tests/test_organ_aging_studio.py
skills/pathway-enricher/SKILL.md
- Network accessline 11
always: false emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 11
always: false emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 12
emoji: 🔬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
homepage: https://github.com/ClawBio/ClawBio - Network accessline 75
1. **Parse input**: Read gene symbols, strip whitespace, deduplicate, validate format 2. **Submit to Enrichr**: POST the gene list to `https://maayanlab.cloud/Enrichr/addList` - Network accessline 75
1. **Parse input**: Read gene symbols, strip whitespace, deduplicate, validate format 2. **Submit to Enrichr**: POST the gene list to `https://maayanlab.cloud/Enrichr/addList` - Network accessline 76
2. **Submit to Enrichr**: POST the gene list to `https://maayanlab.cloud/Enrichr/addList` - Network accessline 76
2. **Submit to Enrichr**: POST the gene list to `https://maayanlab.cloud/Enrichr/addList`
skills/pathway-enricher/pathway_enricher.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 85
ENRICHR_BASE = "https://maayanlab.cloud/Enrichr" - Network accessline 85
ENRICHR_BASE = "https://maayanlab.cloud/Enrichr" - Network accessline 119
"description": (None, description), } resp = requests.post( - Network accessline 119
"description": (None, description), } resp = requests.post( - Network accessline 120
} resp = requests.post( f"{ENRICHR_BASE}/addList", - Network accessline 120
} resp = requests.post( f"{ENRICHR_BASE}/addList", - Network accessline 121
resp = requests.post( - Network accessline 121
resp = requests.post( - Network accessline 148
url = f"{ENRICHR_BASE}/enrich" params = {"userListId": user_list_id, "backgroundType": library} resp = requests.get(url, params=params, timeout=30) - Network accessline 148
url = f"{ENRICHR_BASE}/enrich" params = {"userListId": user_list_id, "backgroundType": library} resp = requests.get(url, params=params, timeout=30) - Network accessline 149
params = {"userListId": user_list_id, "backgroundType": library} resp = requests.get(url, params=params, timeout=30) resp.raise_for_status() - Network accessline 149
params = {"userListId": user_list_id, "backgroundType": library} resp = requests.get(url, params=params, timeout=30) resp.raise_for_status() - Network accessline 150
resp = requests.get(url, params=params, timeout=30) - Network accessline 150
resp = requests.get(url, params=params, timeout=30) - Network accessline 465
sections.append("---\n\n## Methods\n") sections.append( "Enrichment analysis performed using the [Enrichr API](https://maayanlab.cloud/Enrichr). " - Network accessline 465
sections.append("---\n\n## Methods\n") sections.append( "Enrichment analysis performed using the [Enrichr API](https://maayanlab.cloud/Enrichr). " - Network accessline 466
sections.append( "Enrichment analysis performed using the [Enrichr API](https://maayanlab.cloud/Enrichr). " "Combined score = −log(p-value) × z-score (Enrichr's default ranking metric). " - Network accessline 466
sections.append( "Enrichment analysis performed using the [Enrichr API](https://maayanlab.cloud/Enrichr). " "Combined score = −log(p-value) × z-score (Enrichr's default ranking metric). " - Network accessline 467
"Enrichment analysis performed using the [Enrichr API](https://maayanlab.cloud/Enrichr). " - Network accessline 467
"Enrichment analysis performed using the [Enrichr API](https://maayanlab.cloud/Enrichr). "
skills/pathway-enricher/tests/test_pathway_enricher.py
skills/pharmgx-reporter/SKILL.md
- Network accessline 17
always: false emoji: 💊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 17
always: false emoji: 💊 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
emoji: 💊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 18
emoji: 💊 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 153
- [CPIC Guidelines](https://cpicpgx.org/) — Clinical Pharmacogenetics Implementation Consortium - Network accessline 153
- [CPIC Guidelines](https://cpicpgx.org/) — Clinical Pharmacogenetics Implementation Consortium - Network accessline 154
- [CPIC API](https://api.cpicpgx.org/) — diplotype-to-phenotype tables last checked 2026-10-05; DPYD against CPIC's `DPYD_Diplotype_Phenotype_Table.xlsx` (generated 2026-08-07) (`CPIC_TABLES_CHECKED`); CYP1A2 and MTHFR not covered (no CPIC - Network accessline 154
- [CPIC API](https://api.cpicpgx.org/) — diplotype-to-phenotype tables last checked 2026-10-05; DPYD against CPIC's `DPYD_Diplotype_Phenotype_Table.xlsx` (generated 2026-08-07) (`CPIC_TABLES_CHECKED`); CYP1A2 and MTHFR not covered (no CPIC - Network accessline 155
- [FDA Table of Pharmacogenomic Biomarkers](https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling) — FDA-approved PGx drug labels - Network accessline 155
- [FDA Table of Pharmacogenomic Biomarkers](https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling) — FDA-approved PGx drug labels
skills/pharmgx-reporter/api.py
skills/pharmgx-reporter/demo_patient.txt
- Network accessline 1
# Real pharmacogenomic data from Manuel Corpas's publicly available 23andMe # genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 - Network accessline 1
# Real pharmacogenomic data from Manuel Corpas's publicly available 23andMe # genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 - Network accessline 2
# genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 # - Network accessline 2
# genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 # - Network accessline 3
# Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 - Network accessline 3
# Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682
skills/pharmgx-reporter/demo_report/report.md
- Network accessline 226
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 226
- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio - Network accessline 227
- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/ - Network accessline 227
- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/ - Network accessline 228
- Diplotype-to-phenotype tables checked against CPIC (api.cpicpgx.org, 2026-10-05; DPYD against CPIC DPYD_Diplotype_Phenotype_Table.xlsx generated 2026-08-07); CYP1A2 and MTHFR not covered (no CPIC guideline). - Caudle, K.E. et al. (2014). - Network accessline 228
- Diplotype-to-phenotype tables checked against CPIC (api.cpicpgx.org, 2026-10-05; DPYD against CPIC DPYD_Diplotype_Phenotype_Table.xlsx generated 2026-08-07); CYP1A2 and MTHFR not covered (no CPIC guideline). - Caudle, K.E. et al. (2014). - Network accessline 230
- PharmGKB. https://www.pharmgkb.org/ - Network accessline 230
- PharmGKB. https://www.pharmgkb.org/
skills/pharmgx-reporter/evals/019e82fd-c7f1-76ed-9b4b-63bbfd454ebd/scenario-0/inputs/patient_data.txt
- Network accessline 1
# Real pharmacogenomic data from Manuel Corpas's publicly available 23andMe # genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 - Network accessline 1
# Real pharmacogenomic data from Manuel Corpas's publicly available 23andMe # genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 - Network accessline 2
# genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 # - Network accessline 2
# genome (Corpasome, CC0 license). # Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 # - Network accessline 3
# Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682 - Network accessline 3
# Download: https://figshare.com/articles/dataset/23andMe_SNP_chip_genotype_data/92682
skills/pharmgx-reporter/examples/demo_report.html
- Network accessline 295
<div class="disclaimer"><strong>Disclaimer:</strong> ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.</div - Network accessline 295
<div class="disclaimer"><strong>Disclaimer:</strong> ClawBio is a research and educational tool. It is not a medical device and does not provide clinical diagnoses. Consult a healthcare professional before making any medical decisions.</div - Network accessline 296
<div class="report-header"><svg class="header-logo" viewBox="0 0 200 200" xmlns="http://www.w3.org/2000/svg"><g fill="white" fill-rule="evenodd"><path d="M60 30 C55 80, 40 130, 50 170 C55 175, 65 175, 68 168 C78 130, 70 80, 75 35 Z"/><path - Network accessline 296
<div class="report-header"><svg class="header-logo" viewBox="0 0 200 200" xmlns="http://www.w3.org/2000/svg"><g fill="white" fill-rule="evenodd"><path d="M60 30 C55 80, 40 130, 50 170 C55 175, 65 175, 68 168 C78 130, 70 80, 75 35 Z"/><path - Network accessline 297
<div class="exec-summary"><h3>Summary</h3><div class="exec-summary-grid"><div class="exec-stat stat-avoid"><span class="stat-icon">⛔</span><div class="stat-text"><strong>1 drug(s) to avoid</strong><span>Warfarin (Coumadin)</span></div></div - Network accessline 297
<div class="exec-summary"><h3>Summary</h3><div class="exec-summary-grid"><div class="exec-stat stat-avoid"><span class="stat-icon">⛔</span><div class="stat-text"><strong>1 drug(s) to avoid</strong><span>Warfarin (Coumadin)</span></div></div - Network accessline 298
<h2>Drug Recommendations</h2> <div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-avoid"><td><strong>Warfarin</strong> (Coumadin)</td> - Network accessline 298
<h2>Drug Recommendations</h2> <div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-avoid"><td><strong>Warfarin</strong> (Coumadin)</td> - Network accessline 299
<div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-avoid"><td><strong>Warfarin</strong> (Coumadin)</td><td><span class="badge badge-a - Network accessline 299
<div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-avoid"><td><strong>Warfarin</strong> (Coumadin)</td><td><span class="badge badge-a - Network accessline 300
<tr class="row-caution"><td><strong>Amitriptyline</strong> (Elavil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 300
<tr class="row-caution"><td><strong>Amitriptyline</strong> (Elavil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 301
<tr class="row-caution"><td><strong>Celecoxib</strong> (Celebrex)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 301
<tr class="row-caution"><td><strong>Celecoxib</strong> (Celebrex)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 302
<tr class="row-caution"><td><strong>Clomipramine</strong> (Anafranil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 302
<tr class="row-caution"><td><strong>Clomipramine</strong> (Anafranil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 303
<tr class="row-caution"><td><strong>Clopidogrel</strong> (Plavix)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 303
<tr class="row-caution"><td><strong>Clopidogrel</strong> (Plavix)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 304
<tr class="row-caution"><td><strong>Codeine</strong> (Tylenol w/ Codeine)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation C - Network accessline 304
<tr class="row-caution"><td><strong>Codeine</strong> (Tylenol w/ Codeine)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation C - Network accessline 305
<tr class="row-caution"><td><strong>Desipramine</strong> (Norpramin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 305
<tr class="row-caution"><td><strong>Desipramine</strong> (Norpramin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 306
<tr class="row-caution"><td><strong>Doxepin</strong> (Sinequan)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium" - Network accessline 306
<tr class="row-caution"><td><strong>Doxepin</strong> (Sinequan)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium" - Network accessline 307
<tr class="row-caution"><td><strong>Efavirenz</strong> (Sustiva)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium - Network accessline 307
<tr class="row-caution"><td><strong>Efavirenz</strong> (Sustiva)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium - Network accessline 308
<tr class="row-caution"><td><strong>Flurbiprofen</strong> (Ansaid)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 308
<tr class="row-caution"><td><strong>Flurbiprofen</strong> (Ansaid)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 309
<tr class="row-caution"><td><strong>Haloperidol</strong> (Haldol)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-text">Dose adjustment or monitoring may be needed.</span></div></ - Network accessline 309
<tr class="row-caution"><td><strong>Haloperidol</strong> (Haldol)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-text">Dose adjustment or monitoring may be needed.</span></div></ - Network accessline 310
<tr class="row-caution"><td><strong>Hydrocodone</strong> (Vicodin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 310
<tr class="row-caution"><td><strong>Hydrocodone</strong> (Vicodin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 311
<tr class="row-caution"><td><strong>Imipramine</strong> (Tofranil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 311
<tr class="row-caution"><td><strong>Imipramine</strong> (Tofranil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 312
<tr class="row-caution"><td><strong>Meloxicam</strong> (Mobic)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium"> - Network accessline 312
<tr class="row-caution"><td><strong>Meloxicam</strong> (Mobic)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium"> - Network accessline 313
<tr class="row-caution"><td><strong>Nortriptyline</strong> (Pamelor)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 313
<tr class="row-caution"><td><strong>Nortriptyline</strong> (Pamelor)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 314
<tr class="row-caution"><td><strong>Phenytoin</strong> (Dilantin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 314
<tr class="row-caution"><td><strong>Phenytoin</strong> (Dilantin)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 315
<tr class="row-caution"><td><strong>Piroxicam</strong> (Feldene)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium - Network accessline 315
<tr class="row-caution"><td><strong>Piroxicam</strong> (Feldene)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium - Network accessline 316
<tr class="row-caution"><td><strong>Risperidone</strong> (Risperdal)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-text">Dose adjustment or monitoring may be needed.</span></div - Network accessline 316
<tr class="row-caution"><td><strong>Risperidone</strong> (Risperdal)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-text">Dose adjustment or monitoring may be needed.</span></div - Network accessline 317
<tr class="row-caution"><td><strong>Tamoxifen</strong> (Nolvadex)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 317
<tr class="row-caution"><td><strong>Tamoxifen</strong> (Nolvadex)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortiu - Network accessline 318
<tr class="row-caution"><td><strong>Tramadol</strong> (Ultram)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium"> - Network accessline 318
<tr class="row-caution"><td><strong>Tramadol</strong> (Ultram)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consortium"> - Network accessline 319
<tr class="row-caution"><td><strong>Trimipramine</strong> (Surmontil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 319
<tr class="row-caution"><td><strong>Trimipramine</strong> (Surmontil)</td><td><span class="badge badge-caution">Caution</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 320
<details><summary>Standard Drugs (30 medications — click to expand)</summary><div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-stand - Network accessline 320
<details><summary>Standard Drugs (30 medications — click to expand)</summary><div class="table-wrap"><table><thead><tr><th>Drug</th><th>Recommendation</th><th>Evidence</th><th>Class</th><th>Genes</th></tr></thead><tbody><tr class="row-stand - Network accessline 321
<tr class="row-standard"><td><strong>Atazanavir</strong> (Reyataz)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 321
<tr class="row-standard"><td><strong>Atazanavir</strong> (Reyataz)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 322
<tr class="row-standard"><td><strong>Atomoxetine</strong> (Strattera)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 322
<tr class="row-standard"><td><strong>Atomoxetine</strong> (Strattera)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 323
<tr class="row-standard"><td><strong>Atorvastatin</strong> (Lipitor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 323
<tr class="row-standard"><td><strong>Atorvastatin</strong> (Lipitor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 324
<tr class="row-standard"><td><strong>Azathioprine</strong> (Imuran)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 324
<tr class="row-standard"><td><strong>Azathioprine</strong> (Imuran)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 325
<tr class="row-standard"><td><strong>Capecitabine</strong> (Xeloda)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 325
<tr class="row-standard"><td><strong>Capecitabine</strong> (Xeloda)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 326
<tr class="row-standard"><td><strong>Citalopram</strong> (Celexa)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 326
<tr class="row-standard"><td><strong>Citalopram</strong> (Celexa)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 327
<tr class="row-standard"><td><strong>Clozapine</strong> (Clozaril)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 327
<tr class="row-standard"><td><strong>Clozapine</strong> (Clozaril)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 328
<tr class="row-standard"><td><strong>Dexlansoprazole</strong> (Dexilant)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation - Network accessline 328
<tr class="row-standard"><td><strong>Dexlansoprazole</strong> (Dexilant)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation - Network accessline 329
<tr class="row-standard"><td><strong>Escitalopram</strong> (Lexapro)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 329
<tr class="row-standard"><td><strong>Escitalopram</strong> (Lexapro)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 330
<tr class="row-standard"><td><strong>Esomeprazole</strong> (Nexium)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 330
<tr class="row-standard"><td><strong>Esomeprazole</strong> (Nexium)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 331
<tr class="row-standard"><td><strong>Fluorouracil</strong> (5-FU)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 331
<tr class="row-standard"><td><strong>Fluorouracil</strong> (5-FU)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 332
<tr class="row-standard"><td><strong>Fluoxetine</strong> (Prozac)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 332
<tr class="row-standard"><td><strong>Fluoxetine</strong> (Prozac)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 333
<tr class="row-standard"><td><strong>Irinotecan</strong> (Camptosar)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div> - Network accessline 333
<tr class="row-standard"><td><strong>Irinotecan</strong> (Camptosar)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div> - Network accessline 334
<tr class="row-standard"><td><strong>Lansoprazole</strong> (Prevacid)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 334
<tr class="row-standard"><td><strong>Lansoprazole</strong> (Prevacid)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 335
<tr class="row-standard"><td><strong>Mercaptopurine</strong> (Purinethol)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span>< - Network accessline 335
<tr class="row-standard"><td><strong>Mercaptopurine</strong> (Purinethol)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span>< - Network accessline 336
<tr class="row-standard"><td><strong>Metoprolol</strong> (Lopressor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 336
<tr class="row-standard"><td><strong>Metoprolol</strong> (Lopressor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 337
<tr class="row-standard"><td><strong>Omeprazole</strong> (Prilosec)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 337
<tr class="row-standard"><td><strong>Omeprazole</strong> (Prilosec)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 338
<tr class="row-standard"><td><strong>Ondansetron</strong> (Zofran)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 338
<tr class="row-standard"><td><strong>Ondansetron</strong> (Zofran)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 339
<tr class="row-standard"><td><strong>Oxycodone</strong> (OxyContin)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 339
<tr class="row-standard"><td><strong>Oxycodone</strong> (OxyContin)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 340
<tr class="row-standard"><td><strong>Pantoprazole</strong> (Protonix)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 340
<tr class="row-standard"><td><strong>Pantoprazole</strong> (Protonix)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 341
<tr class="row-standard"><td><strong>Paroxetine</strong> (Paxil)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 341
<tr class="row-standard"><td><strong>Paroxetine</strong> (Paxil)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consorti - Network accessline 342
<tr class="row-standard"><td><strong>Pravastatin</strong> (Pravachol)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 342
<tr class="row-standard"><td><strong>Pravastatin</strong> (Pravachol)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Con - Network accessline 343
<tr class="row-standard"><td><strong>Rosuvastatin</strong> (Crestor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 343
<tr class="row-standard"><td><strong>Rosuvastatin</strong> (Crestor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Cons - Network accessline 344
<tr class="row-standard"><td><strong>Sertraline</strong> (Zoloft)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 344
<tr class="row-standard"><td><strong>Sertraline</strong> (Zoloft)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 345
<tr class="row-standard"><td><strong>Simvastatin</strong> (Zocor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 345
<tr class="row-standard"><td><strong>Simvastatin</strong> (Zocor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consort - Network accessline 346
<tr class="row-standard"><td><strong>Tacrolimus</strong> (Prograf)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 346
<tr class="row-standard"><td><strong>Tacrolimus</strong> (Prograf)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div></ - Network accessline 347
<tr class="row-standard"><td><strong>Thioguanine</strong> (Tabloid)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 347
<tr class="row-standard"><td><strong>Thioguanine</strong> (Tabloid)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-text">Standard dosing expected to be effective.</span></div>< - Network accessline 348
<tr class="row-standard"><td><strong>Venlafaxine</strong> (Effexor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 348
<tr class="row-standard"><td><strong>Venlafaxine</strong> (Effexor)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Conso - Network accessline 349
<tr class="row-standard"><td><strong>Voriconazole</strong> (Vfend)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor - Network accessline 349
<tr class="row-standard"><td><strong>Voriconazole</strong> (Vfend)</td><td><span class="badge badge-standard">Standard</span><div class="evidence-recs"><span class="evidence-rec-source" title="Clinical Pharmacogenetics Implementation Consor
skills/pharmgx-reporter/pharmgx_reporter.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
Executable file; content unavailable - Executable scriptline 1
Executable file; content unavailable - Executable scriptline 1
Executable file; content unavailable - Executable scriptline 1
Executable file; content unavailable - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 1004
# # Source: Ensembl release 112 / dbSNP b156. # GRCh38: https://rest.ensembl.org/variation/human/<rsid> - Network accessline 1004
# # Source: Ensembl release 112 / dbSNP b156. # GRCh38: https://rest.ensembl.org/variation/human/<rsid> - Network accessline 1004
# # Source: Ensembl release 112 / dbSNP b156. # GRCh38: https://rest.ensembl.org/variation/human/<rsid> - Network accessline 1005
# Source: Ensembl release 112 / dbSNP b156. # GRCh38: https://rest.ensembl.org/variation/human/<rsid> # GRCh37: https://grch37.rest.ensembl.org/variation/human/<rsid> - Network accessline 1005
# Source: Ensembl release 112 / dbSNP b156. # GRCh38: https://rest.ensembl.org/variation/human/<rsid> # GRCh37: https://grch37.rest.ensembl.org/variation/human/<rsid> - Network accessline 1005
# Source: Ensembl release 112 / dbSNP b156. # GRCh38: https://rest.ensembl.org/variation/human/<rsid> # GRCh37: https://grch37.rest.ensembl.org/variation/human/<rsid> - Network accessline 1006
# GRCh38: https://rest.ensembl.org/variation/human/<rsid> - Network accessline 1006
# GRCh38: https://rest.ensembl.org/variation/human/<rsid> - Network accessline 1006
# GRCh38: https://rest.ensembl.org/variation/human/<rsid> - Network accessline 1007
# GRCh37: https://grch37.rest.ensembl.org/variation/human/<rsid> - Network accessline 1007
# GRCh37: https://grch37.rest.ensembl.org/variation/human/<rsid> - Network accessline 1007
# GRCh37: https://grch37.rest.ensembl.org/variation/human/<rsid> - Network accessline 1906
lines.append("## References") lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1906
lines.append("## References") lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1906
lines.append("## References") lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1907
lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1907
lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1907
lines.append("") lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1908
lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1908
lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1908
lines.append("- Corpas, M. (2026). ClawBio. https://github.com/ClawBio/ClawBio") - Network accessline 1909
lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1909
lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1909
lines.append("- CPIC. Clinical Pharmacogenetics Implementation Consortium. https://cpicpgx.org/") - Network accessline 1911
" CYP1A2 and MTHFR not covered (no CPIC guideline).") lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.phar - Network accessline 1911
" CYP1A2 and MTHFR not covered (no CPIC guideline).") lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.phar - Network accessline 1911
" CYP1A2 and MTHFR not covered (no CPIC guideline).") lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.phar - Network accessline 1912
lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.pharmgkb.org/") lines.append("") - Network accessline 1912
lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.pharmgkb.org/") lines.append("") - Network accessline 1912
lines.append("- Caudle, K.E. et al. (2014). Standardizing terms for clinical pharmacogenetic test results. Genet Med, 16(9), 655-663.") lines.append("- PharmGKB. https://www.pharmgkb.org/") lines.append("") - Network accessline 1913
lines.append("- PharmGKB. https://www.pharmgkb.org/") - Network accessline 1913
lines.append("- PharmGKB. https://www.pharmgkb.org/") - Network accessline 1913
lines.append("- PharmGKB. https://www.pharmgkb.org/") - Network accessline 1938
for rsid, _allele in rsids: lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1938
for rsid, _allele in rsids: lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1938
for rsid, _allele in rsids: lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1939
lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' f'target="_blank" rel="noopener">' - Network accessline 1939
lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' f'target="_blank" rel="noopener">' - Network accessline 1939
lines.append( f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' f'target="_blank" rel="noopener">' - Network accessline 1940
f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1940
f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1940
f'<a href="https://www.clinpgx.org/rsid/{rsid}" ' - Network accessline 1944
if not rsids: lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1944
if not rsids: lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1944
if not rsids: lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1945
lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' f'target="_blank" rel="noopener">{_html.escape(gene)}</a>' - Network accessline 1945
lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' f'target="_blank" rel="noopener">{_html.escape(gene)}</a>' - Network accessline 1945
lines.append( f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' f'target="_blank" rel="noopener">{_html.escape(gene)}</a>' - Network accessline 1946
f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1946
f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" ' - Network accessline 1946
f'<a href="https://www.clinpgx.org/gene/{_html.escape(gene)}" '
skills/pharmgx-reporter/tests/test_pharmgx.py
skills/phylogenetics-builder/SKILL.md
- Network accessline 10
always: false emoji: 🌳 homepage: https://github.com/ClawBio/ClawBio - Network accessline 10
always: false emoji: 🌳 homepage: https://github.com/ClawBio/ClawBio - Network accessline 11
emoji: 🌳 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 11
emoji: 🌳 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 12
homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
homepage: https://github.com/ClawBio/ClawBio - Network accessline 375
- [IQ-TREE 2](https://doi.org/10.1093/molbev/msaa015) — Minh et al., 2020 - Network accessline 375
- [IQ-TREE 2](https://doi.org/10.1093/molbev/msaa015) — Minh et al., 2020 - Network accessline 376
- [RAxML-NG](https://doi.org/10.1093/bioinformatics/btz305) — Kozlov et al., 2019 - Network accessline 376
- [RAxML-NG](https://doi.org/10.1093/bioinformatics/btz305) — Kozlov et al., 2019 - Network accessline 377
- [ModelTest-NG](https://doi.org/10.1093/molbev/msz189) — Darriba et al., 2020 - Network accessline 377
- [ModelTest-NG](https://doi.org/10.1093/molbev/msz189) — Darriba et al., 2020 - Network accessline 378
- [trimAl](https://doi.org/10.1093/bioinformatics/btp348) — Capella-Gutiérrez et al., 2009 - Network accessline 378
- [trimAl](https://doi.org/10.1093/bioinformatics/btp348) — Capella-Gutiérrez et al., 2009 - Network accessline 379
- [MAFFT](https://doi.org/10.1093/molbev/mst010) — Katoh & Standley, 2013 - Network accessline 379
- [MAFFT](https://doi.org/10.1093/molbev/mst010) — Katoh & Standley, 2013 - Network accessline 380
- [MUSCLE v5](https://doi.org/10.1101/2021.06.20.449169) — Edgar, 2021 (bioRxiv); [MUSCLE v3](https://doi.org/10.1093/nar/gkh340) — Edgar, 2004 - Network accessline 380
- [MUSCLE v5](https://doi.org/10.1101/2021.06.20.449169) — Edgar, 2021 (bioRxiv); [MUSCLE v3](https://doi.org/10.1093/nar/gkh340) — Edgar, 2004 - Network accessline 381
- [T-Coffee](https://doi.org/10.1006/jmbi.2000.4042) — Notredame et al., 2000 - Network accessline 381
- [T-Coffee](https://doi.org/10.1006/jmbi.2000.4042) — Notredame et al., 2000 - Network accessline 382
- [ClustalW](https://doi.org/10.1093/nar/22.22.4673) — Thompson et al., 1994 - Network accessline 382
- [ClustalW](https://doi.org/10.1093/nar/22.22.4673) — Thompson et al., 1994 - Network accessline 383
- [KAlign](https://doi.org/10.1186/1471-2105-6-298) — Lassmann & Sonnhammer, 2005 - Network accessline 383
- [KAlign](https://doi.org/10.1186/1471-2105-6-298) — Lassmann & Sonnhammer, 2005 - Network accessline 384
- [PRANK](https://doi.org/10.1126/science.1158395) — Löytynoja & Goldman, 2008 - Network accessline 384
- [PRANK](https://doi.org/10.1126/science.1158395) — Löytynoja & Goldman, 2008 - Network accessline 385
- [ETE3](https://doi.org/10.1093/molbev/msw046) — Huerta-Cepas et al., 2016 - Network accessline 385
- [ETE3](https://doi.org/10.1093/molbev/msw046) — Huerta-Cepas et al., 2016 - Network accessline 386
- [Bio.Phylo](https://doi.org/10.1186/1471-2105-13-209) — Talevich et al., 2012 - Network accessline 386
- [Bio.Phylo](https://doi.org/10.1186/1471-2105-13-209) — Talevich et al., 2012
skills/phylogenetics-builder/api.py
skills/phylogenetics-builder/phylogenetics_builder.py
skills/phylogenetics-builder/tests/test_phylogenetics_builder.py
skills/polars-bio/SKILL.md
- Network accessline 80
always: false emoji: "🐻" homepage: https://github.com/ClawBio/ClawBio - Network accessline 80
always: false emoji: "🐻" homepage: https://github.com/ClawBio/ClawBio - Network accessline 81
emoji: "🐻" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 81
emoji: "🐻" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 82
homepage: https://github.com/ClawBio/ClawBio - Network accessline 82
homepage: https://github.com/ClawBio/ClawBio - Network accessline 333
Wiewiórka M, Khamutou P, Zbysiński M, Gambin T. **polars-bio — fast, scalable, and out-of-core operations on large genomic interval datasets.** *Bioinformatics*, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 333
Wiewiórka M, Khamutou P, Zbysiński M, Gambin T. **polars-bio — fast, scalable, and out-of-core operations on large genomic interval datasets.** *Bioinformatics*, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 335
41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 335
41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640
skills/polars-bio/examples/generate_fixtures.py
skills/polars-bio/polars_bio_runner.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 6
Wraps polars-bio (https://github.com/biodatageeks/polars-bio). - Network accessline 6
Wraps polars-bio (https://github.com/biodatageeks/polars-bio). - Network accessline 9
Citation: Wiewiorka M, Khamutou P, Zbysinski M, Gambin T. polars-bio - fast, scalable, and out-of-core operations on large genomic interval datasets. Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 9
Citation: Wiewiorka M, Khamutou P, Zbysinski M, Gambin T. polars-bio - fast, scalable, and out-of-core operations on large genomic interval datasets. Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 11
Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 11
Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 50
"Wiewiorka M, Khamutou P, Zbysinski M, Gambin T. polars-bio - fast, scalable, " "and out-of-core operations on large genomic interval datasets. " "Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640" - Network accessline 50
"Wiewiorka M, Khamutou P, Zbysinski M, Gambin T. polars-bio - fast, scalable, " "and out-of-core operations on large genomic interval datasets. " "Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640" - Network accessline 51
"and out-of-core operations on large genomic interval datasets. " "Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640" ) - Network accessline 51
"and out-of-core operations on large genomic interval datasets. " "Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640" ) - Network accessline 52
"Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640" - Network accessline 52
"Bioinformatics, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640" - Access to secretsline 66
[Credential-related source omitted] - Access to secretsline 66
[Credential-related source omitted]
skills/polars-bio/references/polars_primer.md
- Network accessline 3
> Citation: Wiewiórka M, Khamutou P, Zbysiński M, Gambin T. **polars-bio — fast, > scalable, and out-of-core operations on large genomic interval datasets.** > *Bioinformatics*, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/b - Network accessline 3
> Citation: Wiewiórka M, Khamutou P, Zbysiński M, Gambin T. **polars-bio — fast, > scalable, and out-of-core operations on large genomic interval datasets.** > *Bioinformatics*, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/b - Network accessline 5
> *Bioinformatics*, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 5
> *Bioinformatics*, 2025, 41(12):btaf640. https://doi.org/10.1093/bioinformatics/btaf640 - Network accessline 12
[Polars](https://pola.rs) is a DataFrame library written in Rust: - Network accessline 12
[Polars](https://pola.rs) is a DataFrame library written in Rust:
skills/polars-bio/tests/test_polars_bio.py
skills/pride-fetch/SKILL.md
- Network accessline 80
always: false emoji: "🧪" homepage: https://www.ebi.ac.uk/pride/archive/ - Network accessline 80
always: false emoji: "🧪" homepage: https://www.ebi.ac.uk/pride/archive/ - Network accessline 81
emoji: "🧪" homepage: https://www.ebi.ac.uk/pride/archive/ os: - Network accessline 81
emoji: "🧪" homepage: https://www.ebi.ac.uk/pride/archive/ os: - Network accessline 82
homepage: https://www.ebi.ac.uk/pride/archive/ - Network accessline 82
homepage: https://www.ebi.ac.uk/pride/archive/ - Network accessline 320
Proteomics RAW files are routinely tens of gigabytes; never run or submit it without telling the user the file count and total size first. It emits only `https://` locations (`ftp://` is rewritten first). Aspera and other - Network accessline 320
Proteomics RAW files are routinely tens of gigabytes; never run or submit it without telling the user the file count and total size first. It emits only `https://` locations (`ftp://` is rewritten first). Aspera and other - Network accessline 321
without telling the user the file count and total size first. It emits only `https://` locations (`ftp://` is rewritten first). Aspera and other non-URL locations are skipped with a warning. This is deliberate: quoting - Network accessline 321
without telling the user the file count and total size first. It emits only `https://` locations (`ftp://` is rewritten first). Aspera and other non-URL locations are skipped with a warning. This is deliberate: quoting - Network accessline 322
`https://` locations (`ftp://` is rewritten first). Aspera and other - Network accessline 322
`https://` locations (`ftp://` is rewritten first). Aspera and other - Network accessline 323
non-URL locations are skipped with a warning. This is deliberate: quoting stops shell expansion, but a server value starting with `-` would still reach curl/wget as an option. `download` likewise refuses non-http(s) URLs. If - Network accessline 323
non-URL locations are skipped with a warning. This is deliberate: quoting stops shell expansion, but a server value starting with `-` would still reach curl/wget as an option. `download` likewise refuses non-http(s) URLs. If - Network accessline 324
stops shell expansion, but a server value starting with `-` would still reach curl/wget as an option. `download` likewise refuses non-http(s) URLs. If every file is skipped, the project has no https location. Report that rather - Network accessline 324
stops shell expansion, but a server value starting with `-` would still reach curl/wget as an option. `download` likewise refuses non-http(s) URLs. If every file is skipped, the project has no https location. Report that rather - Network accessline 325
curl/wget as an option. `download` likewise refuses non-http(s) URLs. If - Network accessline 325
curl/wget as an option. `download` likewise refuses non-http(s) URLs. If - Network accessline 390
- [PRIDE Archive](https://www.ebi.ac.uk/pride/archive/) and its - Network accessline 390
- [PRIDE Archive](https://www.ebi.ac.uk/pride/archive/) and its - Network accessline 391
[REST API v3](https://www.ebi.ac.uk/pride/ws/archive/v3/webjars/swagger-ui/index.html). - Network accessline 391
[REST API v3](https://www.ebi.ac.uk/pride/ws/archive/v3/webjars/swagger-ui/index.html). - Network accessline 392
- [quantms minimal SDRF](https://github.com/bigbio/quantmsdiann/blob/main/docs/usage.md#minimal-valid-metadata-example); - Network accessline 392
- [quantms minimal SDRF](https://github.com/bigbio/quantmsdiann/blob/main/docs/usage.md#minimal-valid-metadata-example); - Network accessline 393
the 19-column contract this skill targets. - Demo fixture: [PXD084218](https://www.ebi.ac.uk/pride/archive/projects/PXD084218), Arabidopsis thaliana proteomics, licensed CC0. - Network accessline 393
the 19-column contract this skill targets. - Demo fixture: [PXD084218](https://www.ebi.ac.uk/pride/archive/projects/PXD084218), Arabidopsis thaliana proteomics, licensed CC0. - Network accessline 394
- Demo fixture: [PXD084218](https://www.ebi.ac.uk/pride/archive/projects/PXD084218), - Network accessline 394
- Demo fixture: [PXD084218](https://www.ebi.ac.uk/pride/archive/projects/PXD084218), - Network accessline 395
Arabidopsis thaliana proteomics, licensed CC0. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 395
Arabidopsis thaliana proteomics, licensed CC0. - Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 396
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`pride/`), © 2026 UK Dementia Research Institute, MIT. - Network accessline 396
- Ported from [UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) @ `7cc3e6e` (`pride/`), © 2026 UK Dementia Research Institute, MIT. - Network accessline 397
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills) - Network accessline 397
[UKDRI/informatics_data_skills](https://github.com/UKDRI/informatics_data_skills)
skills/pride-fetch/examples/demo_PXD084218_project.json
- Network accessline 5
"projectDescription": "Microbes have the potential to provide growth-promoting benefits to plants and crops, but effective plant\u2013microbe partnerships require mechanisms to control microbial activity in a programmable and host-specific - Network accessline 5
"projectDescription": "Microbes have the potential to provide growth-promoting benefits to plants and crops, but effective plant\u2013microbe partnerships require mechanisms to control microbial activity in a programmable and host-specific - Network accessline 6
"sampleProcessingProtocol": "Arabidopsis thaliana seedlings were grown on 1\u00d7 MS Gelzan plates and harvested at 14 days. Shoot and root tissues were separated, weighed, immediately flash-frozen in liquid nitrogen, and stored at \u221280 - Network accessline 6
"sampleProcessingProtocol": "Arabidopsis thaliana seedlings were grown on 1\u00d7 MS Gelzan plates and harvested at 14 days. Shoot and root tissues were separated, weighed, immediately flash-frozen in liquid nitrogen, and stored at \u221280 - Network accessline 7
"dataProcessingProtocol": "MS/MS spectra were searched separately against the Araport11 database Arabidopsis thaliana\u00a0(https://www.arabidopsis.org/), concatenated with decoy protein sequences using the MSFragger 4.1 software by includi - Network accessline 7
"dataProcessingProtocol": "MS/MS spectra were searched separately against the Araport11 database Arabidopsis thaliana\u00a0(https://www.arabidopsis.org/), concatenated with decoy protein sequences using the MSFragger 4.1 software by includi
skills/pride-fetch/pride_fetch.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 61
p.add_argument("--local-dir") p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " - Network accessline 61
p.add_argument("--local-dir") p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " - Network accessline 62
p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " "because it also retries HTTP 403 and aborts a stalled " - Network accessline 62
p.add_argument("--tool", choices=["curl", "wget"], default="curl", help="download-script transfer tool; curl is the default " "because it also retries HTTP 403 and aborts a stalled " - Network accessline 63
help="download-script transfer tool; curl is the default " - Network accessline 63
help="download-script transfer tool; curl is the default " - Network accessline 189
output_dir, title=f"PRIDE report — {accession}", source_url=f"[PRIDE Archive](https://www.ebi.ac.uk/pride/archive/projects/{accession})", - Network accessline 189
output_dir, title=f"PRIDE report — {accession}", source_url=f"[PRIDE Archive](https://www.ebi.ac.uk/pride/archive/projects/{accession})", - Network accessline 190
title=f"PRIDE report — {accession}", source_url=f"[PRIDE Archive](https://www.ebi.ac.uk/pride/archive/projects/{accession})", sections=sections, - Network accessline 190
title=f"PRIDE report — {accession}", source_url=f"[PRIDE Archive](https://www.ebi.ac.uk/pride/archive/projects/{accession})", sections=sections, - Network accessline 191
source_url=f"[PRIDE Archive](https://www.ebi.ac.uk/pride/archive/projects/{accession})", - Network accessline 191
source_url=f"[PRIDE Archive](https://www.ebi.ac.uk/pride/archive/projects/{accession})",
skills/pride-fetch/pride_fetch_api.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Uses the PRIDE Archive REST API v3 (https://www.ebi.ac.uk/pride/ws/archive/v3). File downloads use the public FTP - Network accessline 8
Uses the PRIDE Archive REST API v3 (https://www.ebi.ac.uk/pride/ws/archive/v3). File downloads use the public FTP - Network accessline 9
(https://www.ebi.ac.uk/pride/ws/archive/v3). File downloads use the public FTP - Network accessline 9
(https://www.ebi.ac.uk/pride/ws/archive/v3). File downloads use the public FTP - Network accessline 37
API = "https://www.ebi.ac.uk/pride/ws/archive/v3" - Network accessline 37
API = "https://www.ebi.ac.uk/pride/ws/archive/v3" - Network accessline 40
# Minimal valid SDRF for the quantms / quantmsdiann (DIA-NN) pipeline, in order. # https://github.com/bigbio/quantmsdiann/blob/main/docs/usage.md#minimal-valid-metadata-example - Network accessline 40
# Minimal valid SDRF for the quantms / quantmsdiann (DIA-NN) pipeline, in order. # https://github.com/bigbio/quantmsdiann/blob/main/docs/usage.md#minimal-valid-metadata-example - Network accessline 41
# https://github.com/bigbio/quantmsdiann/blob/main/docs/usage.md#minimal-valid-metadata-example - Network accessline 41
# https://github.com/bigbio/quantmsdiann/blob/main/docs/usage.md#minimal-valid-metadata-example - Network accessline 95
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT, "Accept": "application/json"}) - Network accessline 95
for attempt in range(retries): try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT, "Accept": "application/json"}) - Network accessline 96
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT, "Accept": "application/json"}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 96
try: req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT, "Accept": "application/json"}) with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 97
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT, "Accept": "application/json"}) - Network accessline 97
req = urllib.request.Request(url, headers={"User-Agent": USER_AGENT, "Accept": "application/json"}) - Network accessline 98
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 98
with urllib.request.urlopen(req, timeout=180) as r: - Network accessline 194
return dest print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(dl, headers={"User-Agent": USER_AGENT}) - Network accessline 194
return dest print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(dl, headers={"User-Agent": USER_AGENT}) - Network accessline 195
print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(dl, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 195
print(f" downloading {name} ...", file=sys.stderr) req = urllib.request.Request(dl, headers={"User-Agent": USER_AGENT}) with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 196
req = urllib.request.Request(dl, headers={"User-Agent": USER_AGENT}) - Network accessline 196
req = urllib.request.Request(dl, headers={"User-Agent": USER_AGENT}) - Network accessline 197
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 197
with urllib.request.urlopen(req, timeout=600) as r, open(dest + ".part", "wb") as fh: - Network accessline 258
return (f'curl -fsSL --retry {RETRIES} --retry-delay {RETRY_DELAY} ' - Network accessline 258
return (f'curl -fsSL --retry {RETRIES} --retry-delay {RETRY_DELAY} ' - Network accessline 262
# wget: -q fully quiet, -c to resume. Verified against GNU Wget 1.25.0 on - Network accessline 262
# wget: -q fully quiet, -c to resume. Verified against GNU Wget 1.25.0 on - Network accessline 267
return (f'wget -q --tries={RETRIES} --waitretry={RETRY_DELAY} ' - Network accessline 267
return (f'wget -q --tries={RETRIES} --waitretry={RETRY_DELAY} ' - Network accessline 300
PRIDE data files are typically vendor .raw files or .zip archives (which for Bruker timsTOF data contain .d directories). One quiet curl/wget command is - Network accessline 300
PRIDE data files are typically vendor .raw files or .zip archives (which for Bruker timsTOF data contain .d directories). One quiet curl/wget command is - Network accessline 301
Bruker timsTOF data contain .d directories). One quiet curl/wget command is - Network accessline 301
Bruker timsTOF data contain .d directories). One quiet curl/wget command is - Network accessline 314
# shlex.quote stops shell expansion, not option parsing: a value starting # with `-` (ftp_url falls back to any location) would reach curl/wget as - Network accessline 314
# shlex.quote stops shell expansion, not option parsing: a value starting # with `-` (ftp_url falls back to any location) would reach curl/wget as - Network accessline 315
# with `-` (ftp_url falls back to any location) would reach curl/wget as - Network accessline 315
# with `-` (ftp_url falls back to any location) would reach curl/wget as - Network accessline 624
try: data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 624
try: data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 625
data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) .decode("utf-8", "replace")) - Network accessline 625
data = json.loads( http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) .decode("utf-8", "replace")) - Network accessline 626
http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession) - Network accessline 626
http_get("https://www.ebi.ac.uk/biosamples/samples/" + accession)
skills/pride-fetch/tests/test_pride_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 49
assert api._https("ftp://ftp.pride.ebi.ac.uk/a/b.raw") == \ "https://ftp.pride.ebi.ac.uk/a/b.raw" - Network accessline 49
assert api._https("ftp://ftp.pride.ebi.ac.uk/a/b.raw") == \ "https://ftp.pride.ebi.ac.uk/a/b.raw" - Network accessline 50
"https://ftp.pride.ebi.ac.uk/a/b.raw" - Network accessline 50
"https://ftp.pride.ebi.ac.uk/a/b.raw" - Network accessline 280
transfers = [c for c in calls if "--help" not in c and c[:2] != ["-q", "-o"]] assert [c[-1] for c in transfers] == [ f"https://ftp.pride.ebi.ac.uk/p/{n}" for n in names] - Network accessline 280
transfers = [c for c in calls if "--help" not in c and c[:2] != ["-q", "-o"]] assert [c[-1] for c in transfers] == [ f"https://ftp.pride.ebi.ac.uk/p/{n}" for n in names] - Network accessline 281
assert [c[-1] for c in transfers] == [ f"https://ftp.pride.ebi.ac.uk/p/{n}" for n in names] unzip = [c for c in calls if c[:2] == ["-q", "-o"]] - Network accessline 281
assert [c[-1] for c in transfers] == [ f"https://ftp.pride.ebi.ac.uk/p/{n}" for n in names] unzip = [c for c in calls if c[:2] == ["-q", "-o"]] - Network accessline 282
f"https://ftp.pride.ebi.ac.uk/p/{n}" for n in names] - Network accessline 282
f"https://ftp.pride.ebi.ac.uk/p/{n}" for n in names] - Network accessline 296
"""ftp_url() falls back to the first location of any kind, so a value that starts with `-` would reach curl/wget as an option; shlex.quote does not - Network accessline 296
"""ftp_url() falls back to the first location of any kind, so a value that starts with `-` would reach curl/wget as an option; shlex.quote does not - Network accessline 297
starts with `-` would reach curl/wget as an option; shlex.quote does not - Network accessline 297
starts with `-` would reach curl/wget as an option; shlex.quote does not - Network accessline 312
body = script.read_text() assert value not in body assert "https://ftp.pride.ebi.ac.uk/p/ok.raw" in body - Network accessline 312
body = script.read_text() assert value not in body assert "https://ftp.pride.ebi.ac.uk/p/ok.raw" in body - Network accessline 313
assert value not in body assert "https://ftp.pride.ebi.ac.uk/p/ok.raw" in body assert "skipping" in capsys.readouterr().err - Network accessline 313
assert value not in body assert "https://ftp.pride.ebi.ac.uk/p/ok.raw" in body assert "skipping" in capsys.readouterr().err - Network accessline 314
assert "https://ftp.pride.ebi.ac.uk/p/ok.raw" in body - Network accessline 314
assert "https://ftp.pride.ebi.ac.uk/p/ok.raw" in body
skills/profile-report/SKILL.md
- Network accessline 17
always: false emoji: 📋 homepage: https://github.com/ClawBio/ClawBio - Network accessline 17
always: false emoji: 📋 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
emoji: 📋 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 18
emoji: 📋 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio
skills/profile-report/profile_report.py
skills/profile-report/tests/__init__.py
skills/profile-report/tests/test_profile_report.py
skills/profile-report/tests/test_profile_reproducibility.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 23
[Credential-related source omitted] - Access to secretsline 23
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted] - Access to secretsline 92
[Credential-related source omitted]
skills/proteomics-clock/SKILL.md
- Network accessline 49
always: false emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio - Network accessline 49
always: false emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio - Network accessline 50
emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 50
emoji: 🕰<U+FE0F> homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 51
homepage: https://github.com/ClawBio/ClawBio - Network accessline 51
homepage: https://github.com/ClawBio/ClawBio - Network accessline 259
**Real-world example**: The [Filbin et al. (2021)](https://doi.org/10.1016/J.XCRM.2021.100287) longitudinal COVID-19 Olink dataset (freely available from [Mendeley Data](https://doi.org/10.17632/nf853r8xsj.2)) contains 784 samples across Da - Network accessline 259
**Real-world example**: The [Filbin et al. (2021)](https://doi.org/10.1016/J.XCRM.2021.100287) longitudinal COVID-19 Olink dataset (freely available from [Mendeley Data](https://doi.org/10.17632/nf853r8xsj.2)) contains 784 samples across Da - Network accessline 280
- [Goeminne et al. (2025)](https://doi.org/10.1016/j.cmet.2024.10.005) Cell Metabolism 37(1):205-222.e6 — organ-specific proteomic aging clocks - Network accessline 280
- [Goeminne et al. (2025)](https://doi.org/10.1016/j.cmet.2024.10.005) Cell Metabolism 37(1):205-222.e6 — organ-specific proteomic aging clocks - Network accessline 281
- [organAging GitHub](https://github.com/ludgergoeminne/organAging) — model coefficients and example scripts - Network accessline 281
- [organAging GitHub](https://github.com/ludgergoeminne/organAging) — model coefficients and example scripts - Network accessline 282
- [Olink Proteomics](https://olink.com) — Proximity Extension Assay platform - Network accessline 282
- [Olink Proteomics](https://olink.com) — Proximity Extension Assay platform
skills/proteomics-clock/examples/fetch_filbin.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Data source: https://doi.org/10.17632/nf853r8xsj.2 (Mendeley Data, free) - Network accessline 8
Data source: https://doi.org/10.17632/nf853r8xsj.2 (Mendeley Data, free) - Network accessline 36
for p in [olink_path, meta_path, supp_path]: if not p.exists(): print(f"ERROR: Missing {p.name}. Download from https://doi.org/10.17632/nf853r8xsj.2") - Network accessline 36
for p in [olink_path, meta_path, supp_path]: if not p.exists(): print(f"ERROR: Missing {p.name}. Download from https://doi.org/10.17632/nf853r8xsj.2") - Network accessline 37
if not p.exists(): print(f"ERROR: Missing {p.name}. Download from https://doi.org/10.17632/nf853r8xsj.2") sys.exit(1) - Network accessline 37
if not p.exists(): print(f"ERROR: Missing {p.name}. Download from https://doi.org/10.17632/nf853r8xsj.2") sys.exit(1) - Network accessline 38
print(f"ERROR: Missing {p.name}. Download from https://doi.org/10.17632/nf853r8xsj.2") - Network accessline 38
print(f"ERROR: Missing {p.name}. Download from https://doi.org/10.17632/nf853r8xsj.2")
skills/proteomics-clock/examples/treatment_effect_covid.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 8
Prerequisites: 1. Download Filbin data from https://doi.org/10.17632/nf853r8xsj.2 - Network accessline 8
Prerequisites: 1. Download Filbin data from https://doi.org/10.17632/nf853r8xsj.2 - Network accessline 9
1. Download Filbin data from https://doi.org/10.17632/nf853r8xsj.2 - Network accessline 9
1. Download Filbin data from https://doi.org/10.17632/nf853r8xsj.2
skills/proteomics-clock/proteomics_clock.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 43
ORGANAGING_COMMIT = "5147b0301ec7f4abdb10ef650d04f47454ddc8fd" GITHUB_RAW_BASE = ( f"https://raw.githubusercontent.com/ludgergoeminne/organAging/{ORGANAGING_COMMIT}/data/output_Python" - Network accessline 43
ORGANAGING_COMMIT = "5147b0301ec7f4abdb10ef650d04f47454ddc8fd" GITHUB_RAW_BASE = ( f"https://raw.githubusercontent.com/ludgergoeminne/organAging/{ORGANAGING_COMMIT}/data/output_Python" - Network accessline 44
GITHUB_RAW_BASE = ( f"https://raw.githubusercontent.com/ludgergoeminne/organAging/{ORGANAGING_COMMIT}/data/output_Python" ) - Network accessline 44
GITHUB_RAW_BASE = ( f"https://raw.githubusercontent.com/ludgergoeminne/organAging/{ORGANAGING_COMMIT}/data/output_Python" ) - Network accessline 45
f"https://raw.githubusercontent.com/ludgergoeminne/organAging/{ORGANAGING_COMMIT}/data/output_Python" - Network accessline 45
f"https://raw.githubusercontent.com/ludgergoeminne/organAging/{ORGANAGING_COMMIT}/data/output_Python" - Access to secretsline 72
[Credential-related source omitted] - Access to secretsline 72
[Credential-related source omitted] - Network accessline 183
) return cached.read_text() resp = requests.get(url, timeout=30) - Network accessline 183
) return cached.read_text() resp = requests.get(url, timeout=30) - Network accessline 184
return cached.read_text() resp = requests.get(url, timeout=30) resp.raise_for_status() - Network accessline 184
return cached.read_text() resp = requests.get(url, timeout=30) resp.raise_for_status() - Network accessline 185
resp = requests.get(url, timeout=30) - Network accessline 185
resp = requests.get(url, timeout=30)
skills/proteomics-clock/tests/test_proteomics_clock.py
skills/proteomics-de/SKILL.md
- Network accessline 12
always: false emoji: 🥚 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🥚 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🥚 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
emoji: 🥚 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio
skills/proteomics-de/proteomics_de.py
skills/proteomics-de/tests/test_proteomics_de.py
skills/protocols-io/SKILL.md
- Network accessline 21
always: false emoji: 🧪 homepage: https://www.protocols.io - Network accessline 21
always: false emoji: 🧪 homepage: https://www.protocols.io - Network accessline 22
emoji: 🧪 homepage: https://www.protocols.io os: - Network accessline 22
emoji: 🧪 homepage: https://www.protocols.io os: - Network accessline 23
homepage: https://www.protocols.io - Network accessline 23
homepage: https://www.protocols.io - Network accessline 42
You are **Protocols.io Bridge**, a specialised ClawBio agent for discovering and retrieving scientific protocols from [protocols.io](https://www.protocols.io). Your role is to search, browse, and fetch full protocol details — including step - Network accessline 42
You are **Protocols.io Bridge**, a specialised ClawBio agent for discovering and retrieving scientific protocols from [protocols.io](https://www.protocols.io). Your role is to search, browse, and fetch full protocol details — including step - Access to secretsline 52
[Credential-related source omitted] - Access to secretsline 52
[Credential-related source omitted] - Access to secretsline 70
[Credential-related source omitted] - Access to secretsline 70
[Credential-related source omitted] - Access to secretsline 78
[Credential-related source omitted] - Access to secretsline 78
[Credential-related source omitted] - Network accessline 107
1. Go to [protocols.io/developers](https://www.protocols.io/developers) - Network accessline 107
1. Go to [protocols.io/developers](https://www.protocols.io/developers) - Access to secretsline 109
[Credential-related source omitted] - Access to secretsline 109
[Credential-related source omitted] - Access to secretsline 123
[Credential-related source omitted] - Access to secretsline 123
[Credential-related source omitted] - Network accessline 171
- [protocols.io](https://www.protocols.io) — Open access repository for scientific methods - Network accessline 171
- [protocols.io](https://www.protocols.io) — Open access repository for scientific methods - Network accessline 172
- [protocols.io API v3 Documentation](https://apidocs.protocols.io/) — REST API reference - Network accessline 172
- [protocols.io API v3 Documentation](https://apidocs.protocols.io/) — REST API reference
skills/protocols-io/protocols_io.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 80
write_portable_commands_sh, ) API_V3 = "https://www.protocols.io/api/v3" - Network accessline 80
write_portable_commands_sh, ) API_V3 = "https://www.protocols.io/api/v3" - Network accessline 81
) API_V3 = "https://www.protocols.io/api/v3" API_V4 = "https://www.protocols.io/api/v4" - Network accessline 81
) API_V3 = "https://www.protocols.io/api/v3" API_V4 = "https://www.protocols.io/api/v4" - Network accessline 82
API_V3 = "https://www.protocols.io/api/v3" API_V4 = "https://www.protocols.io/api/v4" RATE_LIMIT = 100 # requests per 60-second window (protocols.io API) - Network accessline 82
API_V3 = "https://www.protocols.io/api/v3" API_V4 = "https://www.protocols.io/api/v4" RATE_LIMIT = 100 # requests per 60-second window (protocols.io API) - Network accessline 83
API_V4 = "https://www.protocols.io/api/v4" RATE_LIMIT = 100 # requests per 60-second window (protocols.io API) RATE_WINDOW = 60.0 - Network accessline 83
API_V4 = "https://www.protocols.io/api/v4" RATE_LIMIT = 100 # requests per 60-second window (protocols.io API) RATE_WINDOW = 60.0 - Access to secretsline 130
[Credential-related source omitted] - Access to secretsline 130
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Access to secretsline 131
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Access to secretsline 132
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Access to secretsline 142
[Credential-related source omitted] - Network accessline 156
try: resp = requests.get(url, headers=hdrs, params=params, timeout=30) - Network accessline 156
try: resp = requests.get(url, headers=hdrs, params=params, timeout=30) - Network accessline 157
resp = requests.get(url, headers=hdrs, params=params, timeout=30) - Network accessline 157
resp = requests.get(url, headers=hdrs, params=params, timeout=30) - Access to secretsline 183
[Credential-related source omitted] - Access to secretsline 183
[Credential-related source omitted] - Network accessline 227
""" Extract a usable protocol identifier from various input formats: - Full URL: https://www.protocols.io/view/some-protocol-slug-abc123 → some-protocol-slug-abc123 - Network accessline 227
""" Extract a usable protocol identifier from various input formats: - Full URL: https://www.protocols.io/view/some-protocol-slug-abc123 → some-protocol-slug-abc123 - Network accessline 228
Extract a usable protocol identifier from various input formats: - Full URL: https://www.protocols.io/view/some-protocol-slug-abc123 → some-protocol-slug-abc123 - URI slug: some-protocol-slug-abc123 → some-protocol-slug-abc123 - Network accessline 228
Extract a usable protocol identifier from various input formats: - Full URL: https://www.protocols.io/view/some-protocol-slug-abc123 → some-protocol-slug-abc123 - URI slug: some-protocol-slug-abc123 → some-protocol-slug-abc123 - Network accessline 229
- Full URL: https://www.protocols.io/view/some-protocol-slug-abc123 → some-protocol-slug-abc123 - Network accessline 229
- Full URL: https://www.protocols.io/view/some-protocol-slug-abc123 → some-protocol-slug-abc123 - Network accessline 288
pub_str = datetime.fromtimestamp(published, tz=timezone.utc).strftime("%Y-%m-%d") if published else "Draft" n_steps = p.get("number_of_steps") or p.get("stats", {}).get("number_of_steps", "?") url = f"https://www.protocols.i - Network accessline 288
pub_str = datetime.fromtimestamp(published, tz=timezone.utc).strftime("%Y-%m-%d") if published else "Draft" n_steps = p.get("number_of_steps") or p.get("stats", {}).get("number_of_steps", "?") url = f"https://www.protocols.i - Network accessline 290
url = f"https://www.protocols.io/view/{uri}" if uri else "" - Network accessline 290
url = f"https://www.protocols.io/view/{uri}" if uri else "" - Network accessline 326
url = f"https://www.protocols.io/view/{uri}" if uri else "" - Network accessline 326
url = f"https://www.protocols.io/view/{uri}" if uri else "" - Network accessline 555
""" Download protocol PDF from https://www.protocols.io/view/{uri}.pdf - Network accessline 555
""" Download protocol PDF from https://www.protocols.io/view/{uri}.pdf - Network accessline 556
Download protocol PDF from https://www.protocols.io/view/{uri}.pdf - Network accessline 556
Download protocol PDF from https://www.protocols.io/view/{uri}.pdf - Network accessline 559
url = f"https://www.protocols.io/view/{uri}.pdf" - Network accessline 559
url = f"https://www.protocols.io/view/{uri}.pdf" - Access to secretsline 560
[Credential-related source omitted] - Access to secretsline 560
[Credential-related source omitted] - Network accessline 565
try: resp = requests.get(url, headers=hdrs, timeout=60) - Network accessline 565
try: resp = requests.get(url, headers=hdrs, timeout=60) - Network accessline 566
resp = requests.get(url, headers=hdrs, timeout=60) - Network accessline 566
resp = requests.get(url, headers=hdrs, timeout=60) - Access to secretsline 618
[Credential-related source omitted] - Access to secretsline 618
[Credential-related source omitted] - Network accessline 620
print( "ERROR: No access token. Set PROTOCOLS_IO_ACCESS_TOKEN " "(get one at https://www.protocols.io/developers).", - Network accessline 620
print( "ERROR: No access token. Set PROTOCOLS_IO_ACCESS_TOKEN " "(get one at https://www.protocols.io/developers).", - Network accessline 621
[Credential-related source omitted] - Network accessline 621
[Credential-related source omitted] - Access to secretsline 621
[Credential-related source omitted] - Access to secretsline 621
[Credential-related source omitted] - Network accessline 622
"(get one at https://www.protocols.io/developers).", - Network accessline 622
"(get one at https://www.protocols.io/developers).",
skills/protocols-io/tests/test_protocols_io.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 30
[Credential-related source omitted] - Access to secretsline 30
[Credential-related source omitted] - Network accessline 94
data = _load_demo_json("demo_search_results.json") md = format_search_results(data, "test") assert "https://www.protocols.io/view/" in md - Network accessline 94
data = _load_demo_json("demo_search_results.json") md = format_search_results(data, "test") assert "https://www.protocols.io/view/" in md - Network accessline 96
assert "https://www.protocols.io/view/" in md - Network accessline 96
assert "https://www.protocols.io/view/" in md - Access to secretsline 229
[Credential-related source omitted] - Access to secretsline 229
[Credential-related source omitted] - Access to secretsline 230
[Credential-related source omitted] - Access to secretsline 230
[Credential-related source omitted] - Access to secretsline 231
[Credential-related source omitted] - Access to secretsline 231
[Credential-related source omitted] - Access to secretsline 232
[Credential-related source omitted] - Access to secretsline 232
[Credential-related source omitted] - Network accessline 242
result = _parse_protocol_id("https://www.protocols.io/view/one-blot-western-grhbv36") - Network accessline 242
result = _parse_protocol_id("https://www.protocols.io/view/one-blot-western-grhbv36") - Network accessline 248
result = _parse_protocol_id("https://www.protocols.io/view/some-protocol-abc123/") - Network accessline 248
result = _parse_protocol_id("https://www.protocols.io/view/some-protocol-abc123/") - Network accessline 254
result = _parse_protocol_id("https://www.protocols.io/view/my-proto-xyz?version=2&foo=bar") - Network accessline 254
result = _parse_protocol_id("https://www.protocols.io/view/my-proto-xyz?version=2&foo=bar") - Access to secretsline 308
[Credential-related source omitted] - Access to secretsline 308
[Credential-related source omitted] - Access to secretsline 324
[Credential-related source omitted] - Access to secretsline 324
[Credential-related source omitted] - Access to secretsline 340
[Credential-related source omitted] - Access to secretsline 340
[Credential-related source omitted] - Access to secretsline 356
[Credential-related source omitted] - Access to secretsline 356
[Credential-related source omitted] - Access to secretsline 371
[Credential-related source omitted] - Access to secretsline 371
[Credential-related source omitted] - Access to secretsline 386
[Credential-related source omitted] - Access to secretsline 386
[Credential-related source omitted] - Access to secretsline 401
[Credential-related source omitted] - Access to secretsline 401
[Credential-related source omitted] - Network accessline 435
assert "](https://www.protocols.io/view/" not in md - Network accessline 435
assert "](https://www.protocols.io/view/" not in md - Network accessline 436
assert "https://www.protocols.io/view/" in md - Network accessline 436
assert "https://www.protocols.io/view/" in md - Access to secretsline 450
[Credential-related source omitted] - Access to secretsline 450
[Credential-related source omitted] - Access to secretsline 465
[Credential-related source omitted] - Access to secretsline 465
[Credential-related source omitted] - Access to secretsline 479
[Credential-related source omitted] - Access to secretsline 479
[Credential-related source omitted] - Access to secretsline 525
[Credential-related source omitted] - Access to secretsline 525
[Credential-related source omitted] - Access to secretsline 540
[Credential-related source omitted] - Access to secretsline 540
[Credential-related source omitted] - Access to secretsline 555
[Credential-related source omitted] - Access to secretsline 555
[Credential-related source omitted] - Access to secretsline 572
[Credential-related source omitted] - Access to secretsline 572
[Credential-related source omitted] - Access to secretsline 585
[Credential-related source omitted] - Access to secretsline 585
[Credential-related source omitted] - Access to secretsline 704
[Credential-related source omitted] - Access to secretsline 704
[Credential-related source omitted] - Access to secretsline 721
[Credential-related source omitted] - Access to secretsline 721
[Credential-related source omitted] - Access to secretsline 746
[Credential-related source omitted] - Access to secretsline 746
[Credential-related source omitted]
skills/prs-abstain/SKILL.md
- Network accessline 82
always: false emoji: "🚦" homepage: https://github.com/ClawBio/ClawBio - Network accessline 82
always: false emoji: "🚦" homepage: https://github.com/ClawBio/ClawBio - Network accessline 83
emoji: "🚦" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 83
emoji: "🚦" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 84
homepage: https://github.com/ClawBio/ClawBio - Network accessline 84
homepage: https://github.com/ClawBio/ClawBio - Network accessline 450
- [Kosoy et al. 2009, Hum Mutat 30:69-78](https://pubmed.ncbi.nlm.nih.gov/18683858/); validated - Network accessline 450
- [Kosoy et al. 2009, Hum Mutat 30:69-78](https://pubmed.ncbi.nlm.nih.gov/18683858/); validated - Network accessline 451
continental assignment with AIM subsets down to 24. The skill's floor of 30 sits above it. - [Martin et al. 2019, Nat Genet 51:584-591](https://pubmed.ncbi.nlm.nih.gov/30926966/); polygenic score transferability collapses outside the disc - Network accessline 451
continental assignment with AIM subsets down to 24. The skill's floor of 30 sits above it. - [Martin et al. 2019, Nat Genet 51:584-591](https://pubmed.ncbi.nlm.nih.gov/30926966/); polygenic score transferability collapses outside the disc - Network accessline 452
- [Martin et al. 2019, Nat Genet 51:584-591](https://pubmed.ncbi.nlm.nih.gov/30926966/); - Network accessline 452
- [Martin et al. 2019, Nat Genet 51:584-591](https://pubmed.ncbi.nlm.nih.gov/30926966/); - Network accessline 453
polygenic score transferability collapses outside the discovery population. - [PGS Catalog](https://www.pgscatalog.org/); source of the scores and their reference populations. - [Duncan et al. 2019, Nat Commun 10:3328](https://pubmed.ncbi.n - Network accessline 453
polygenic score transferability collapses outside the discovery population. - [PGS Catalog](https://www.pgscatalog.org/); source of the scores and their reference populations. - [Duncan et al. 2019, Nat Commun 10:3328](https://pubmed.ncbi.n - Network accessline 454
- [PGS Catalog](https://www.pgscatalog.org/); source of the scores and their reference populations. - Network accessline 454
- [PGS Catalog](https://www.pgscatalog.org/); source of the scores and their reference populations. - Network accessline 455
- [Duncan et al. 2019, Nat Commun 10:3328](https://pubmed.ncbi.nlm.nih.gov/31346163/); - Network accessline 455
- [Duncan et al. 2019, Nat Commun 10:3328](https://pubmed.ncbi.nlm.nih.gov/31346163/);
skills/prs-abstain/pdf_report.py
skills/prs-abstain/prs_abstain.py
skills/prs-abstain/tests/fixtures/PGS000001_hmPOS_GRCh37_authentic.txt
skills/prs-abstain/tests/test_prs_abstain.py
skills/prs-applicability-gate/SKILL.md
- Network accessline 54
always: false emoji: "🚦" homepage: https://github.com/rinatrizvanov/prsguard-demo - Network accessline 54
always: false emoji: "🚦" homepage: https://github.com/rinatrizvanov/prsguard-demo - Network accessline 55
emoji: "🚦" homepage: https://github.com/rinatrizvanov/prsguard-demo os: - Network accessline 55
emoji: "🚦" homepage: https://github.com/rinatrizvanov/prsguard-demo os: - Network accessline 56
homepage: https://github.com/rinatrizvanov/prsguard-demo - Network accessline 56
homepage: https://github.com/rinatrizvanov/prsguard-demo - Network accessline 214
**Key parameters** (`config/calibration.yaml`, `calibration_version` `2026.09.26-3`; derivations and experiments in [PRSGuard `docs/calibration.md`](https://github.com/rinatrizvanov/prsguard-demo/blob/v1.0.1/docs/calibration.md)): - Network accessline 214
**Key parameters** (`config/calibration.yaml`, `calibration_version` `2026.09.26-3`; derivations and experiments in [PRSGuard `docs/calibration.md`](https://github.com/rinatrizvanov/prsguard-demo/blob/v1.0.1/docs/calibration.md)): - Network accessline 215
[PRSGuard `docs/calibration.md`](https://github.com/rinatrizvanov/prsguard-demo/blob/v1.0.1/docs/calibration.md)): - Network accessline 215
[PRSGuard `docs/calibration.md`](https://github.com/rinatrizvanov/prsguard-demo/blob/v1.0.1/docs/calibration.md)): - Network accessline 382
- [PGS Catalog](https://www.pgscatalog.org/) (Lambert et al., Nat Genet 2021); score metadata, evaluations, - Network accessline 382
- [PGS Catalog](https://www.pgscatalog.org/) (Lambert et al., Nat Genet 2021); score metadata, evaluations, - Network accessline 383
harmonised scoring files - [1000 Genomes Project phase 3](https://www.internationalgenome.org/) (Nature 2015); reference super-populations - [pgsc_calc](https://github.com/PGScatalog/pgsc_calc) (Lambert et al., Nat Genet 2024); default excl - Network accessline 383
harmonised scoring files - [1000 Genomes Project phase 3](https://www.internationalgenome.org/) (Nature 2015); reference super-populations - [pgsc_calc](https://github.com/PGScatalog/pgsc_calc) (Lambert et al., Nat Genet 2024); default excl - Network accessline 384
- [1000 Genomes Project phase 3](https://www.internationalgenome.org/) (Nature 2015); reference super-populations - Network accessline 384
- [1000 Genomes Project phase 3](https://www.internationalgenome.org/) (Nature 2015); reference super-populations - Network accessline 385
- [pgsc_calc](https://github.com/PGScatalog/pgsc_calc) (Lambert et al., Nat Genet 2024); default exclusion of - Network accessline 385
- [pgsc_calc](https://github.com/PGScatalog/pgsc_calc) (Lambert et al., Nat Genet 2024); default exclusion of - Network accessline 389
- Brown, Cai & DasGupta, Stat Sci 2001; Jeffreys interval that the upstream percentile step uses for finite-panel uncertainty (the source of `reference_sensitive`) - [PRSGuard](https://github.com/rinatrizvanov/prsguard-demo); the full pip - Network accessline 389
- Brown, Cai & DasGupta, Stat Sci 2001; Jeffreys interval that the upstream percentile step uses for finite-panel uncertainty (the source of `reference_sensitive`) - [PRSGuard](https://github.com/rinatrizvanov/prsguard-demo); the full pip - Network accessline 390
uncertainty (the source of `reference_sensitive`) - [PRSGuard](https://github.com/rinatrizvanov/prsguard-demo); the full pipeline, calibration experiments and benchmarks this skill comes from - Network accessline 390
uncertainty (the source of `reference_sensitive`) - [PRSGuard](https://github.com/rinatrizvanov/prsguard-demo); the full pipeline, calibration experiments and benchmarks this skill comes from - Network accessline 391
- [PRSGuard](https://github.com/rinatrizvanov/prsguard-demo); the full pipeline, calibration experiments and - Network accessline 391
- [PRSGuard](https://github.com/rinatrizvanov/prsguard-demo); the full pipeline, calibration experiments and
skills/prs-applicability-gate/prs_applicability_gate.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 11
Originally developed in PRSGuard (ClawBio Boston Hackathon, Challenge 3): https://github.com/rinatrizvanov/prsguard-demo - Network accessline 11
Originally developed in PRSGuard (ClawBio Boston Hackathon, Challenge 3): https://github.com/rinatrizvanov/prsguard-demo - Network accessline 12
https://github.com/rinatrizvanov/prsguard-demo - Network accessline 12
https://github.com/rinatrizvanov/prsguard-demo
skills/prs-applicability-gate/tests/test_prs_applicability_gate.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Possible obfuscationline 761
@pytest.mark.parametrize("content", ["not json at all", "[1, 2, 3]", "", "<U+FEFF>{\"schema\": 1}"]) - Possible obfuscationline 761
@pytest.mark.parametrize("content", ["not json at all", "[1, 2, 3]", "", "<U+FEFF>{\"schema\": 1}"])
skills/pubmed-summariser/SKILL.md
- Network accessline 31
always: false emoji: 📄 homepage: https://pubmed.ncbi.nlm.nih.gov/ - Network accessline 31
always: false emoji: 📄 homepage: https://pubmed.ncbi.nlm.nih.gov/ - Network accessline 32
emoji: 📄 homepage: https://pubmed.ncbi.nlm.nih.gov/ os: - Network accessline 32
emoji: 📄 homepage: https://pubmed.ncbi.nlm.nih.gov/ os: - Network accessline 33
homepage: https://pubmed.ncbi.nlm.nih.gov/ - Network accessline 33
homepage: https://pubmed.ncbi.nlm.nih.gov/ - Access to secretsline 99
[Credential-related source omitted] - Access to secretsline 99
[Credential-related source omitted]
skills/pubmed-summariser/abstract_summary.py
skills/pubmed-summariser/examples/.env.example
- Access to secretsline 1
[Credential-related source omitted] - Access to secretsline 1
[Credential-related source omitted] - Access to secretsline 2
[Credential-related source omitted] - Access to secretsline 2
[Credential-related source omitted] - Network accessline 5
[Credential-related source omitted] - Network accessline 5
[Credential-related source omitted] - Access to secretsline 5
[Credential-related source omitted] - Access to secretsline 5
[Credential-related source omitted] - Network accessline 7
# OPENAI_BASE_URL=https://api.openai.com/v1 - Network accessline 7
# OPENAI_BASE_URL=https://api.openai.com/v1 - Network accessline 9
# Ollama (no API key required for the default local server) OLLAMA_MODEL=qwen3.5:4b # OLLAMA_BASE_URL=http://localhost:11434/v1 - Network accessline 9
# Ollama (no API key required for the default local server) OLLAMA_MODEL=qwen3.5:4b # OLLAMA_BASE_URL=http://localhost:11434/v1 - Network accessline 11
# OLLAMA_BASE_URL=http://localhost:11434/v1 - Network accessline 11
# OLLAMA_BASE_URL=http://localhost:11434/v1
skills/pubmed-summariser/examples/README.md
- Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 22
[Credential-related source omitted] - Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 24
[Credential-related source omitted] - Access to secretsline 33
[Credential-related source omitted] - Access to secretsline 33
[Credential-related source omitted] - Network accessline 63
Use parameters supported by your model. An empty dictionary uses server defaults. The provider defaults to `http://localhost:11434/v1`; `OLLAMA_BASE_URL` overrides it. - Network accessline 63
Use parameters supported by your model. An empty dictionary uses server defaults. The provider defaults to `http://localhost:11434/v1`; `OLLAMA_BASE_URL` overrides it. - Network accessline 64
The provider defaults to `http://localhost:11434/v1`; `OLLAMA_BASE_URL` overrides it. - Network accessline 64
The provider defaults to `http://localhost:11434/v1`; `OLLAMA_BASE_URL` overrides it. - Access to secretsline 66
[Credential-related source omitted] - Access to secretsline 66
[Credential-related source omitted] - Access to secretsline 67
[Credential-related source omitted] - Access to secretsline 67
[Credential-related source omitted]
skills/pubmed-summariser/examples/run_briefing.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 46
[Credential-related source omitted] - Access to secretsline 46
[Credential-related source omitted] - Access to secretsline 47
[Credential-related source omitted] - Access to secretsline 47
[Credential-related source omitted]
skills/pubmed-summariser/pubmed_api.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 29
_ESEARCH = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 29
_ESEARCH = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 30
_EFETCH = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" - Network accessline 30
_EFETCH = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi" - Network accessline 147
"abstract_sections": sections, "pmid": pmid, "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/", - Network accessline 147
"abstract_sections": sections, "pmid": pmid, "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/", - Network accessline 148
"pmid": pmid, "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/", } - Network accessline 148
"pmid": pmid, "url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/", } - Network accessline 149
"url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/", - Network accessline 149
"url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/", - Network accessline 180
"retmode": "json", } resp = requests.get(_ESEARCH, params=search_params, timeout=_TIMEOUT) - Network accessline 180
"retmode": "json", } resp = requests.get(_ESEARCH, params=search_params, timeout=_TIMEOUT) - Network accessline 181
} resp = requests.get(_ESEARCH, params=search_params, timeout=_TIMEOUT) resp.raise_for_status() - Network accessline 181
} resp = requests.get(_ESEARCH, params=search_params, timeout=_TIMEOUT) resp.raise_for_status() - Network accessline 182
resp = requests.get(_ESEARCH, params=search_params, timeout=_TIMEOUT) - Network accessline 182
resp = requests.get(_ESEARCH, params=search_params, timeout=_TIMEOUT) - Network accessline 196
"retmode": "xml", } resp = requests.get(_EFETCH, params=fetch_params, timeout=_TIMEOUT) - Network accessline 196
"retmode": "xml", } resp = requests.get(_EFETCH, params=fetch_params, timeout=_TIMEOUT) - Network accessline 197
} resp = requests.get(_EFETCH, params=fetch_params, timeout=_TIMEOUT) resp.raise_for_status() - Network accessline 197
} resp = requests.get(_EFETCH, params=fetch_params, timeout=_TIMEOUT) resp.raise_for_status() - Network accessline 198
resp = requests.get(_EFETCH, params=fetch_params, timeout=_TIMEOUT) - Network accessline 198
resp = requests.get(_EFETCH, params=fetch_params, timeout=_TIMEOUT)
skills/pubmed-summariser/pubmed_summariser.py
skills/pubmed-summariser/tests/__init__.py
skills/pubmed-summariser/tests/fixtures/sample_papers.json
- Network accessline 7
"abstract": "BRCA1 and BRCA2 are involved in the repair of DNA double-strand breaks.", "pmid": "26130008", "url": "https://pubmed.ncbi.nlm.nih.gov/26130008/" - Network accessline 7
"abstract": "BRCA1 and BRCA2 are involved in the repair of DNA double-strand breaks.", "pmid": "26130008", "url": "https://pubmed.ncbi.nlm.nih.gov/26130008/" - Network accessline 8
"pmid": "26130008", "url": "https://pubmed.ncbi.nlm.nih.gov/26130008/" }, - Network accessline 8
"pmid": "26130008", "url": "https://pubmed.ncbi.nlm.nih.gov/26130008/" }, - Network accessline 9
"url": "https://pubmed.ncbi.nlm.nih.gov/26130008/" - Network accessline 9
"url": "https://pubmed.ncbi.nlm.nih.gov/26130008/" - Network accessline 16
"abstract": "This is the first sentence.", "pmid": "99999999", "url": "https://pubmed.ncbi.nlm.nih.gov/99999999/" - Network accessline 16
"abstract": "This is the first sentence.", "pmid": "99999999", "url": "https://pubmed.ncbi.nlm.nih.gov/99999999/" - Network accessline 17
"pmid": "99999999", "url": "https://pubmed.ncbi.nlm.nih.gov/99999999/" } - Network accessline 17
"pmid": "99999999", "url": "https://pubmed.ncbi.nlm.nih.gov/99999999/" } - Network accessline 18
"url": "https://pubmed.ncbi.nlm.nih.gov/99999999/" - Network accessline 18
"url": "https://pubmed.ncbi.nlm.nih.gov/99999999/"
skills/pubmed-summariser/tests/test_pubmed_api.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 161
result = _parse_article(article) assert result["pmid"] == "99887766" assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/99887766/" - Network accessline 161
result = _parse_article(article) assert result["pmid"] == "99887766" assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/99887766/" - Network accessline 163
assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/99887766/" - Network accessline 163
assert result["url"] == "https://pubmed.ncbi.nlm.nih.gov/99887766/"
skills/pubmed-summariser/tests/test_pubmed_summariser.py
skills/pubmed-summariser/tests/test_workflow.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 94
provider.name = "ollama" provider.model = "test-model" provider.base_url = "http://localhost:11434/v1" - Network accessline 94
provider.name = "ollama" provider.model = "test-model" provider.base_url = "http://localhost:11434/v1" - Network accessline 95
provider.model = "test-model" provider.base_url = "http://localhost:11434/v1" generated = GenerationResult("The finding needs replication.", "ollama", "test-model", "stop", 200, 12) - Network accessline 95
provider.model = "test-model" provider.base_url = "http://localhost:11434/v1" generated = GenerationResult("The finding needs replication.", "ollama", "test-model", "stop", 200, 12) - Network accessline 96
provider.base_url = "http://localhost:11434/v1" - Network accessline 96
provider.base_url = "http://localhost:11434/v1" - Access to secretsline 149
[Credential-related source omitted] - Access to secretsline 149
[Credential-related source omitted] - Network accessline 186
def test_fetch_failure_does_not_write_success_report(services, tmp_path): services.side_effect = requests.ConnectionError("offline") - Network accessline 186
def test_fetch_failure_does_not_write_success_report(services, tmp_path): services.side_effect = requests.ConnectionError("offline") - Network accessline 187
services.side_effect = requests.ConnectionError("offline") - Network accessline 187
services.side_effect = requests.ConnectionError("offline") - Network accessline 222
provider = Mock() provider.model = "resolved-model" provider.base_url = "http://localhost:11434/v1" - Network accessline 222
provider = Mock() provider.model = "resolved-model" provider.base_url = "http://localhost:11434/v1" - Network accessline 223
provider.model = "resolved-model" provider.base_url = "http://localhost:11434/v1" provider.generate.return_value = GenerationResult("Short summary.", "ollama", "resolved-model", "stop") - Network accessline 223
provider.model = "resolved-model" provider.base_url = "http://localhost:11434/v1" provider.generate.return_value = GenerationResult("Short summary.", "ollama", "resolved-model", "stop") - Network accessline 224
provider.base_url = "http://localhost:11434/v1" - Network accessline 224
provider.base_url = "http://localhost:11434/v1" - Network accessline 233
def test_provider_closed_when_pubmed_fails(services, tmp_path, monkeypatch): services.side_effect = requests.ConnectionError("offline") - Network accessline 233
def test_provider_closed_when_pubmed_fails(services, tmp_path, monkeypatch): services.side_effect = requests.ConnectionError("offline") - Network accessline 234
services.side_effect = requests.ConnectionError("offline") - Network accessline 234
services.side_effect = requests.ConnectionError("offline")
skills/rare-disease-rnaseq/SKILL.md
- Network accessline 12
always: false emoji: 🩸 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🩸 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🩸 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
emoji: 🩸 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio
skills/rare-disease-rnaseq/rare_disease_rnaseq.py
skills/rare-disease-rnaseq/tests/test_rare_disease_rnaseq.py
skills/rare-high-impact-variants/SKILL.md
- Network accessline 46
- python3 always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 46
- python3 always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 47
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 47
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 48
homepage: https://github.com/ClawBio/ClawBio - Network accessline 48
homepage: https://github.com/ClawBio/ClawBio
skills/rare-high-impact-variants/api.py
skills/rare-high-impact-variants/rare_high_impact_variants.py
skills/rare-high-impact-variants/tests/test_logic.py
skills/rare-high-impact-variants/tests/test_rare_high_impact_variants.py
skills/recombinator/SKILL.md
- Network accessline 19
always: false emoji: 🧪 homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
always: false emoji: 🧪 homepage: https://github.com/ClawBio/ClawBio - Network accessline 20
emoji: 🧪 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 20
emoji: 🧪 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 21
homepage: https://github.com/ClawBio/ClawBio - Network accessline 21
homepage: https://github.com/ClawBio/ClawBio
skills/recombinator/recombinator.py
skills/repro-enforcer/SKILL.md
- Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
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homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio
skills/rnaseq-de/SKILL.md
- Network accessline 21
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 21
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 22
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 22
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 23
homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
homepage: https://github.com/ClawBio/ClawBio
skills/rnaseq-de/rnaseq_de.py
skills/rnaseq-de/tests/test_rnaseq_de.py
skills/sample-qc-triage/SKILL.md
- Network accessline 43
always: false emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 43
always: false emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio - Network accessline 44
emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 44
emoji: "🔬" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 45
homepage: https://github.com/ClawBio/ClawBio - Network accessline 45
homepage: https://github.com/ClawBio/ClawBio
skills/sample-qc-triage/sample_qc_triage.py
skills/sample-qc-triage/tests/test_sample_qc_triage.py
skills/scrna-embedding/SKILL.md
- Network accessline 23
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 24
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
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homepage: https://github.com/ClawBio/ClawBio - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 218
- [scvi-tools documentation](https://docs.scvi-tools.org/) — model API and training interface. - Network accessline 218
- [scvi-tools documentation](https://docs.scvi-tools.org/) — model API and training interface. - Network accessline 219
- [Scanpy documentation](https://scanpy.readthedocs.io/) — downstream AnnData analysis utilities. - Network accessline 219
- [Scanpy documentation](https://scanpy.readthedocs.io/) — downstream AnnData analysis utilities. - Network accessline 220
- [AnnData documentation](https://anndata.readthedocs.io/) — single-cell data model. - Network accessline 220
- [AnnData documentation](https://anndata.readthedocs.io/) — single-cell data model.
skills/scrna-embedding/scrna_embedding.py
skills/scrna-embedding/tests/test_scrna_embedding.py
skills/scrna-orchestrator/SKILL.md
- Network accessline 23
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 24
emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 24
emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 25
homepage: https://github.com/ClawBio/ClawBio - Network accessline 275
- [Scanpy documentation](https://scanpy.readthedocs.io/) — analysis API and methods. - Network accessline 275
- [Scanpy documentation](https://scanpy.readthedocs.io/) — analysis API and methods. - Network accessline 276
- [AnnData documentation](https://anndata.readthedocs.io/) — data model. - Network accessline 276
- [AnnData documentation](https://anndata.readthedocs.io/) — data model. - Network accessline 277
- [Leiden algorithm paper](https://www.nature.com/articles/s41598-019-41695-z) — community detection. - Network accessline 277
- [Leiden algorithm paper](https://www.nature.com/articles/s41598-019-41695-z) — community detection. - Network accessline 278
- [Scrublet paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1736-8) — computational doublet detection. - Network accessline 278
- [Scrublet paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1736-8) — computational doublet detection. - Network accessline 279
- [CellTypist documentation](https://www.celltypist.org/) — model-based immune and general cell annotation. - Network accessline 279
- [CellTypist documentation](https://www.celltypist.org/) — model-based immune and general cell annotation.
skills/scrna-orchestrator/scrna_orchestrator.py
skills/scrna-orchestrator/tests/test_scrna_orchestrator.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 30
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[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted]
skills/seq-wrangler/README.md
- Network accessline 5
Part of the [ClawBio](https://github.com/ClawBio/ClawBio) bioinformatics AI agent skill library. - Network accessline 5
Part of the [ClawBio](https://github.com/ClawBio/ClawBio) bioinformatics AI agent skill library. - Network accessline 102
Contributed by [Daniel Garbozo](https://github.com/DanielGarbozo) — resolves [Issue #10](https://github.com/ClawBio/ClawBio/issues/10). - Network accessline 102
Contributed by [Daniel Garbozo](https://github.com/DanielGarbozo) — resolves [Issue #10](https://github.com/ClawBio/ClawBio/issues/10).
skills/seq-wrangler/SKILL.md
- Network accessline 7
requires: always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 7
requires: always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 8
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 8
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 9
homepage: https://github.com/ClawBio/ClawBio - Network accessline 9
homepage: https://github.com/ClawBio/ClawBio
skills/seq-wrangler/seq_wrangler.py
skills/seq-wrangler/tests/test_seq_wrangler.py
skills/skill-builder/SKILL.md
- Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🦖 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
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homepage: https://github.com/ClawBio/ClawBio - Network accessline 14
homepage: https://github.com/ClawBio/ClawBio - Network accessline 206
- [CONTRIBUTING.md](https://github.com/ClawBio/ClawBio/blob/main/CONTRIBUTING.md) — skill submission guidelines and checklist - Network accessline 206
- [CONTRIBUTING.md](https://github.com/ClawBio/ClawBio/blob/main/CONTRIBUTING.md) — skill submission guidelines and checklist - Network accessline 207
- [templates/SKILL-TEMPLATE.md](https://github.com/ClawBio/ClawBio/blob/main/templates/SKILL-TEMPLATE.md) — canonical SKILL.md template - Network accessline 207
- [templates/SKILL-TEMPLATE.md](https://github.com/ClawBio/ClawBio/blob/main/templates/SKILL-TEMPLATE.md) — canonical SKILL.md template
skills/skill-builder/skill_builder.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
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[Credential-related source omitted] - Network accessline 680
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homepage: https://github.com/ClawBio/ClawBio - Dangerous shell operationline 1920
rm ~/.clawbio_skill_builder_draft.json - Dangerous shell operationline 1920
rm ~/.clawbio_skill_builder_draft.json
skills/skill-builder/tests/test_skill_builder.py
skills/spatial-transcriptomics/SKILL.md
- Network accessline 56
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homepage: https://github.com/ClawBio/ClawBio - Network accessline 337
- Wolf, Angerer and Theis (2018) Genome Biol 19:15. PMID 29409532. Scanpy. - Moran (1950) Biometrika 37:17–23. Global Moran's I. - Palla et al. (2022) Nat Methods 19:171–178. [PMID 35102346](https://pubmed.ncbi.nlm.nih.gov/35102346/). [DOI - Network accessline 337
- Wolf, Angerer and Theis (2018) Genome Biol 19:15. PMID 29409532. Scanpy. - Moran (1950) Biometrika 37:17–23. Global Moran's I. - Palla et al. (2022) Nat Methods 19:171–178. [PMID 35102346](https://pubmed.ncbi.nlm.nih.gov/35102346/). [DOI - Network accessline 338
- Moran (1950) Biometrika 37:17–23. Global Moran's I. - Palla et al. (2022) Nat Methods 19:171–178. [PMID 35102346](https://pubmed.ncbi.nlm.nih.gov/35102346/). [DOI 10.1038/s41592-021-01358-2](https://doi.org/10.1038/s41592-021-01358-2). Sq - Network accessline 338
- Moran (1950) Biometrika 37:17–23. Global Moran's I. - Palla et al. (2022) Nat Methods 19:171–178. [PMID 35102346](https://pubmed.ncbi.nlm.nih.gov/35102346/). [DOI 10.1038/s41592-021-01358-2](https://doi.org/10.1038/s41592-021-01358-2). Sq - Network accessline 339
- Palla et al. (2022) Nat Methods 19:171–178. [PMID 35102346](https://pubmed.ncbi.nlm.nih.gov/35102346/). [DOI 10.1038/s41592-021-01358-2](https://doi.org/10.1038/s41592-021-01358-2). Squidpy. - Network accessline 339
- Palla et al. (2022) Nat Methods 19:171–178. [PMID 35102346](https://pubmed.ncbi.nlm.nih.gov/35102346/). [DOI 10.1038/s41592-021-01358-2](https://doi.org/10.1038/s41592-021-01358-2). Squidpy. - Network accessline 340
- [Squidpy 1.6.0 co-occurrence source](https://github.com/scverse/squidpy/blob/v1.6.0/src/squidpy/gr/_ppatterns.py): cumulative radii and eligible-pair marginals; explicit thresholds are required for numeric comparisons. - Network accessline 340
- [Squidpy 1.6.0 co-occurrence source](https://github.com/scverse/squidpy/blob/v1.6.0/src/squidpy/gr/_ppatterns.py): cumulative radii and eligible-pair marginals; explicit thresholds are required for numeric comparisons.
skills/spatial-transcriptomics/examples/public_visium_validation.md
skills/spatial-transcriptomics/fixtures/generate_squidpy_v1_6_fixture.py
skills/spatial-transcriptomics/spatial_report.py
skills/spatial-transcriptomics/spatial_stats.py
skills/spatial-transcriptomics/spatial_transcriptomics.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 43
PUBLIC_VISIUM_ID = "V1_Human_Lymph_Node" PUBLIC_VISIUM_MATRIX_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 43
PUBLIC_VISIUM_ID = "V1_Human_Lymph_Node" PUBLIC_VISIUM_MATRIX_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 44
PUBLIC_VISIUM_MATRIX_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" "V1_Human_Lymph_Node/V1_Human_Lymph_Node_filtered_feature_bc_matrix.tar.gz" - Network accessline 44
PUBLIC_VISIUM_MATRIX_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" "V1_Human_Lymph_Node/V1_Human_Lymph_Node_filtered_feature_bc_matrix.tar.gz" - Network accessline 45
"https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 45
"https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 47
) PUBLIC_VISIUM_SPATIAL_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 47
) PUBLIC_VISIUM_SPATIAL_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 48
PUBLIC_VISIUM_SPATIAL_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" "V1_Human_Lymph_Node/V1_Human_Lymph_Node_spatial.tar.gz" - Network accessline 48
PUBLIC_VISIUM_SPATIAL_URL = ( "https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" "V1_Human_Lymph_Node/V1_Human_Lymph_Node_spatial.tar.gz" - Network accessline 49
"https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 49
"https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/" - Network accessline 379
) as temporary: pending = Path(temporary) / path.name urllib.request.urlretrieve(url, pending) - Network accessline 379
) as temporary: pending = Path(temporary) / path.name urllib.request.urlretrieve(url, pending) - Network accessline 380
pending = Path(temporary) / path.name urllib.request.urlretrieve(url, pending) if sha256_file(pending) != expected: - Network accessline 380
pending = Path(temporary) / path.name urllib.request.urlretrieve(url, pending) if sha256_file(pending) != expected: - Network accessline 381
urllib.request.urlretrieve(url, pending) - Network accessline 381
urllib.request.urlretrieve(url, pending)
skills/spatial-transcriptomics/tests/test_spatial_regressions.py
skills/spatial-transcriptomics/tests/test_spatial_report.py
skills/spatial-transcriptomics/tests/test_spatial_stats.py
skills/spatial-transcriptomics/tests/test_spatial_transcriptomics.py
skills/struct-predictor/SKILL.md
- Network accessline 15
always: false emoji: 🧱 homepage: https://github.com/ClawBio/ClawBio - Network accessline 15
always: false emoji: 🧱 homepage: https://github.com/ClawBio/ClawBio - Network accessline 16
emoji: 🧱 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 16
emoji: 🧱 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 17
homepage: https://github.com/ClawBio/ClawBio - Network accessline 17
homepage: https://github.com/ClawBio/ClawBio - Network accessline 151
- The model will want to `pip install openfold3` and run it. Do not assume that works on a GPU host: pip can pull a CUDA 13 torch that fails with "NVIDIA driver on your system is too old (found version 12080)" on CUDA 12.8 drivers. Check `n - Network accessline 151
- The model will want to `pip install openfold3` and run it. Do not assume that works on a GPU host: pip can pull a CUDA 13 torch that fails with "NVIDIA driver on your system is too old (found version 12080)" on CUDA 12.8 drivers. Check `n - Network accessline 168
- Passaro S et al. (2025) *Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction*. bioRxiv. doi:10.1101/2025.06.14.659707. PMID: 40667369; PMCID: PMC12262699. - Wohlwend J et al. (2024) *Boltz-1: Democratizing Biomolecular Int - Network accessline 168
- Passaro S et al. (2025) *Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction*. bioRxiv. doi:10.1101/2025.06.14.659707. PMID: 40667369; PMCID: PMC12262699. - Wohlwend J et al. (2024) *Boltz-1: Democratizing Biomolecular Int - Network accessline 169
- Wohlwend J et al. (2024) *Boltz-1: Democratizing Biomolecular Interaction Modeling*. bioRxiv. doi:10.1101/2024.11.19.624167 - OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3 - Abramson J et al. (2024) *Accurat - Network accessline 169
- Wohlwend J et al. (2024) *Boltz-1: Democratizing Biomolecular Interaction Modeling*. bioRxiv. doi:10.1101/2024.11.19.624167 - OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3 - Abramson J et al. (2024) *Accurat - Network accessline 170
- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3 - Network accessline 170
- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3
skills/struct-predictor/struct_predictor.py
skills/struct-predictor/struct_predictor_core/__init__.py
skills/struct-predictor/struct_predictor_core/confidence.py
skills/struct-predictor/struct_predictor_core/io.py
skills/struct-predictor/struct_predictor_core/predict.py
skills/struct-predictor/struct_predictor_core/report.py
- Executable scriptline 1
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Executable file - Network accessline 34
"package": "openfold3", "citations": [ "- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3", - Network accessline 34
"package": "openfold3", "citations": [ "- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3", - Network accessline 35
"citations": [ "- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3", "- Abramson J et al. (2024) *Accurate structure prediction of biomolecular interactions with AlphaFold 3*. Nature. doi: - Network accessline 35
"citations": [ "- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3", "- Abramson J et al. (2024) *Accurate structure prediction of biomolecular interactions with AlphaFold 3*. Nature. doi: - Network accessline 36
"- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3", - Network accessline 36
"- OpenFold Consortium. *OpenFold3*. https://github.com/aqlaboratory/openfold-3",
skills/struct-predictor/struct_predictor_core/viewer.py
- Executable scriptline 1
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Executable file - Network accessline 15
_CDN_URL = "https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.1.0/3Dmol-min.js" - Network accessline 15
_CDN_URL = "https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.1.0/3Dmol-min.js" - Network accessline 30
try: import urllib.request js = urllib.request.urlopen(_CDN_URL, timeout=15).read().decode() - Network accessline 30
try: import urllib.request js = urllib.request.urlopen(_CDN_URL, timeout=15).read().decode() - Network accessline 31
import urllib.request js = urllib.request.urlopen(_CDN_URL, timeout=15).read().decode() _CACHE_PATH.parent.mkdir(parents=True, exist_ok=True) - Network accessline 31
import urllib.request js = urllib.request.urlopen(_CDN_URL, timeout=15).read().decode() _CACHE_PATH.parent.mkdir(parents=True, exist_ok=True) - Network accessline 32
js = urllib.request.urlopen(_CDN_URL, timeout=15).read().decode() - Network accessline 32
js = urllib.request.urlopen(_CDN_URL, timeout=15).read().decode()
skills/struct-predictor/tests/__init__.py
skills/struct-predictor/tests/test_struct_predictor.py
skills/target-validation-scorer/SKILL.md
- Network accessline 46
always: false emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio - Network accessline 46
always: false emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio - Network accessline 47
emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 47
emoji: 🎯 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 48
homepage: https://github.com/ClawBio/ClawBio - Network accessline 48
homepage: https://github.com/ClawBio/ClawBio
skills/target-validation-scorer/commands.sh
skills/target-validation-scorer/target_validation_scorer.py
skills/target-validation-scorer/tests/test_target_validation_scorer.py
skills/turingdb-graph/SKILL.md
- Network accessline 70
always: false emoji: 🕸 homepage: https://github.com/ClawBio/ClawBio - Network accessline 70
always: false emoji: 🕸 homepage: https://github.com/ClawBio/ClawBio - Network accessline 71
emoji: 🕸 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 71
emoji: 🕸 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 72
homepage: https://github.com/ClawBio/ClawBio - Network accessline 72
homepage: https://github.com/ClawBio/ClawBio - Network accessline 197
| Flag | Default | Description | |------|---------|-------------| | `--host` | `http://localhost:6666` | TuringDB host URL | - Network accessline 197
| Flag | Default | Description | |------|---------|-------------| | `--host` | `http://localhost:6666` | TuringDB host URL | - Network accessline 198
|------|---------|-------------| | `--host` | `http://localhost:6666` | TuringDB host URL | | `--data-dir` | `~/.turing` | TuringDB data directory | - Network accessline 198
|------|---------|-------------| | `--host` | `http://localhost:6666` | TuringDB host URL | | `--data-dir` | `~/.turing` | TuringDB data directory | - Network accessline 199
| `--host` | `http://localhost:6666` | TuringDB host URL | - Network accessline 199
| `--host` | `http://localhost:6666` | TuringDB host URL | - Network accessline 367
- [TuringDB](https://turingdb.ai); columnar graph database with git-like versioning - Network accessline 367
- [TuringDB](https://turingdb.ai); columnar graph database with git-like versioning - Network accessline 368
- [openCypher](https://opencypher.org); query language specification that TuringDB implements a subset of - Network accessline 368
- [openCypher](https://opencypher.org); query language specification that TuringDB implements a subset of
skills/turingdb-graph/http_server.py
- Executable scriptline 1
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#!/usr/bin/env python3 - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 48
[Credential-related source omitted] - Access to secretsline 49
[Credential-related source omitted] - Access to secretsline 49
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 50
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[Credential-related source omitted] - Access to secretsline 51
[Credential-related source omitted]
skills/turingdb-graph/reference/startup.md
- Network accessline 29
try: client = TuringDB(host="http://localhost:6666") - Network accessline 29
try: client = TuringDB(host="http://localhost:6666") - Network accessline 30
client = TuringDB(host="http://localhost:6666") - Network accessline 30
client = TuringDB(host="http://localhost:6666") - Network accessline 39
Note: `host` is the full URL (`http://localhost:6666`), not a hostname with a separate `port` argument. - Network accessline 39
Note: `host` is the full URL (`http://localhost:6666`), not a hostname with a separate `port` argument. - Network accessline 79
client = TuringDB(host="http://localhost:6666") - Network accessline 79
client = TuringDB(host="http://localhost:6666") - Network accessline 115
client = TuringDB(host="http://localhost:6666") - Network accessline 115
client = TuringDB(host="http://localhost:6666")
skills/turingdb-graph/reference/writing.md
skills/turingdb-graph/tests/test_turingdb_graph.py
skills/turingdb-graph/turingdb_graph.py
skills/ukb-navigator/SKILL.md
- Network accessline 12
always: false emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio - Network accessline 12
always: false emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio - Network accessline 13
emoji: 🏥 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 13
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homepage: https://github.com/ClawBio/ClawBio
skills/ukb-navigator/tests/test_ukb_navigator.py
skills/ukb-navigator/ukb_navigator.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 50
[Credential-related source omitted] - Access to secretsline 51
[Credential-related source omitted] - Access to secretsline 51
[Credential-related source omitted] - Access to secretsline 61
[Credential-related source omitted] - Access to secretsline 61
[Credential-related source omitted]
skills/ukb-ppp-region-fetch/SKILL.md
- Network accessline 61
env: - name: SYNAPSE_AUTH_TOKEN description: Free Synapse personal access token. Required for the file-download path; not required for the listing-only smoke test. Obtain via https://www.synapse.org/Profile:settings ("Personal Acc - Network accessline 61
env: - name: SYNAPSE_AUTH_TOKEN description: Free Synapse personal access token. Required for the file-download path; not required for the listing-only smoke test. Obtain via https://www.synapse.org/Profile:settings ("Personal Acc - Network accessline 62
[Credential-related source omitted] - Network accessline 62
[Credential-related source omitted] - Access to secretsline 62
[Credential-related source omitted] - Access to secretsline 62
[Credential-related source omitted] - Network accessline 63
description: Free Synapse personal access token. Required for the file-download path; not required for the listing-only smoke test. Obtain via https://www.synapse.org/Profile:settings ("Personal Access Tokens"). No UKB Application required - Network accessline 63
description: Free Synapse personal access token. Required for the file-download path; not required for the listing-only smoke test. Obtain via https://www.synapse.org/Profile:settings ("Personal Access Tokens"). No UKB Application required - Network accessline 66
- examples/sort1_ukb_ppp_eur.json endpoints: - https://repo-prod.prod.sagebase.org/repo/v1/ # Synapse REST (listing, file download) - Network accessline 66
- examples/sort1_ukb_ppp_eur.json endpoints: - https://repo-prod.prod.sagebase.org/repo/v1/ # Synapse REST (listing, file download) - Network accessline 67
endpoints: - https://repo-prod.prod.sagebase.org/repo/v1/ # Synapse REST (listing, file download) - s3://ukbiobank.opendata.sagebase.org # AWS Open Data Registry mirror (gated) - Network accessline 67
endpoints: - https://repo-prod.prod.sagebase.org/repo/v1/ # Synapse REST (listing, file download) - s3://ukbiobank.opendata.sagebase.org # AWS Open Data Registry mirror (gated) - Network accessline 68
- https://repo-prod.prod.sagebase.org/repo/v1/ # Synapse REST (listing, file download) - Network accessline 68
- https://repo-prod.prod.sagebase.org/repo/v1/ # Synapse REST (listing, file download) - Access to secretsline 75
[Credential-related source omitted] - Access to secretsline 75
[Credential-related source omitted] - Network accessline 77
always: false emoji: "🧪" homepage: https://github.com/ClawBio/ClawBio - Network accessline 77
always: false emoji: "🧪" homepage: https://github.com/ClawBio/ClawBio - Network accessline 78
emoji: "🧪" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 78
emoji: "🧪" homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 79
homepage: https://github.com/ClawBio/ClawBio - Network accessline 79
homepage: https://github.com/ClawBio/ClawBio - Network accessline 103
2. **Live Synapse fetch (free PAT required).** For arbitrary queries beyond the bundled demo cohort, the skill falls through to a live Synapse downloader. UKB-PPP's AWS Open Data Registry bucket advertises anonymous access but in practice r - Network accessline 103
2. **Live Synapse fetch (free PAT required).** For arbitrary queries beyond the bundled demo cohort, the skill falls through to a live Synapse downloader. UKB-PPP's AWS Open Data Registry bucket advertises anonymous access but in practice r - Network accessline 107
1. Register a free account at <https://www.synapse.org>. - Network accessline 107
1. Register a free account at <https://www.synapse.org>. - Network accessline 108
2. Accept the Synapse Terms of Use (one-time click-through). 3. Open <https://www.synapse.org/Profile:settings> → "Personal Access Tokens". 4. Click "Create new token". Tick scopes `view` and `download`. Copy the token immediately (Sy - Network accessline 108
2. Accept the Synapse Terms of Use (one-time click-through). 3. Open <https://www.synapse.org/Profile:settings> → "Personal Access Tokens". 4. Click "Create new token". Tick scopes `view` and `download`. Copy the token immediately (Sy - Network accessline 109
3. Open <https://www.synapse.org/Profile:settings> → "Personal Access Tokens". 4. Click "Create new token". Tick scopes `view` and `download`. Copy the token immediately (Synapse shows it once). 5. Export it: `export SYNAPSE_AUTH_TOKE - Network accessline 109
3. Open <https://www.synapse.org/Profile:settings> → "Personal Access Tokens". 4. Click "Create new token". Tick scopes `view` and `download`. Copy the token immediately (Synapse shows it once). 5. Export it: `export SYNAPSE_AUTH_TOKE - Access to secretsline 111
[Credential-related source omitted] - Access to secretsline 111
[Credential-related source omitted] - Access to secretsline 154
[Credential-related source omitted] - Access to secretsline 154
[Credential-related source omitted] - Access to secretsline 158
[Credential-related source omitted] - Access to secretsline 158
[Credential-related source omitted] - Access to secretsline 165
[Credential-related source omitted] - Access to secretsline 165
[Credential-related source omitted] - Network accessline 192
[Credential-related source omitted] - Network accessline 192
[Credential-related source omitted] - Access to secretsline 192
[Credential-related source omitted] - Access to secretsline 192
[Credential-related source omitted] - Network accessline 229
- Sun, B.B., Chiou, J., Traylor, M. et al. (2023). *Plasma proteomic associations with genetics and health in the UK Biobank.* Nature 622, 329–338. doi:10.1038/s41586-023-06592-6 (PMID 37794186). - UKB-PPP data release: <https://www.synapse - Network accessline 229
- Sun, B.B., Chiou, J., Traylor, M. et al. (2023). *Plasma proteomic associations with genetics and health in the UK Biobank.* Nature 622, 329–338. doi:10.1038/s41586-023-06592-6 (PMID 37794186). - UKB-PPP data release: <https://www.synapse - Network accessline 230
- UKB-PPP data release: <https://www.synapse.org/Synapse:syn51364943> (Sage Bionetworks, CC-BY 4.0). - Network accessline 230
- UKB-PPP data release: <https://www.synapse.org/Synapse:syn51364943> (Sage Bionetworks, CC-BY 4.0). - Network accessline 231
- REGENIE: Mbatchou, J. et al. (2021). *Computationally efficient whole-genome regression for quantitative and binary traits.* Nat Genet 53, 1097–1103. - Olink Explore 3072 panel content: <https://olink.com/products-services/explore/>. - `s - Network accessline 231
- REGENIE: Mbatchou, J. et al. (2021). *Computationally efficient whole-genome regression for quantitative and binary traits.* Nat Genet 53, 1097–1103. - Olink Explore 3072 panel content: <https://olink.com/products-services/explore/>. - `s - Network accessline 232
- Olink Explore 3072 panel content: <https://olink.com/products-services/explore/>. - Network accessline 232
- Olink Explore 3072 panel content: <https://olink.com/products-services/explore/>.
skills/ukb-ppp-region-fetch/bundled_slices/README.md
skills/ukb-ppp-region-fetch/examples/expected_output.md
- Network accessline 10
# Or live Synapse fetch (PAT required only if you ask for a region the - Network accessline 10
# Or live Synapse fetch (PAT required only if you ask for a region the - Access to secretsline 12
[Credential-related source omitted] - Access to secretsline 12
[Credential-related source omitted] - Network accessline 52
PMID 37794186 (Results: discovery cohort and non-European pQTL mapping).' synapse_id: syn51469328 source_url: https://www.synapse.org/Synapse:syn51469328 - Network accessline 52
PMID 37794186 (Results: discovery cohort and non-European pQTL mapping).' synapse_id: syn51469328 source_url: https://www.synapse.org/Synapse:syn51469328 - Network accessline 53
synapse_id: syn51469328 source_url: https://www.synapse.org/Synapse:syn51469328 fetched_at_utc: '2026-05-15T18:00:00Z' - Network accessline 53
synapse_id: syn51469328 source_url: https://www.synapse.org/Synapse:syn51469328 fetched_at_utc: '2026-05-15T18:00:00Z' - Network accessline 54
source_url: https://www.synapse.org/Synapse:syn51469328 - Network accessline 54
source_url: https://www.synapse.org/Synapse:syn51469328
skills/ukb-ppp-region-fetch/tests/conftest.py
skills/ukb-ppp-region-fetch/tests/test_live_ukb_ppp_region_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 5
[Credential-related source omitted] - Access to secretsline 5
[Credential-related source omitted] - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 56
[Credential-related source omitted] - Access to secretsline 57
[Credential-related source omitted] - Access to secretsline 57
[Credential-related source omitted]
skills/ukb-ppp-region-fetch/tests/test_ukb_ppp_region_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 5
[Credential-related source omitted] - Access to secretsline 5
[Credential-related source omitted] - Network accessline 441
`bundled_slices_dir` is pointed at an empty tmp dir so the client falls through to the live-fetch (mocked) path, bypassing any real - Network accessline 441
`bundled_slices_dir` is pointed at an empty tmp dir so the client falls through to the live-fetch (mocked) path, bypassing any real - Network accessline 442
falls through to the live-fetch (mocked) path, bypassing any real - Network accessline 442
falls through to the live-fetch (mocked) path, bypassing any real - Network accessline 575
n_samples=33_628, synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", - Network accessline 575
n_samples=33_628, synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", - Network accessline 576
synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", n_samples_min=33_628, - Network accessline 576
synapse_id="syn52362400", source_url="https://www.synapse.org/Synapse:syn52362400", n_samples_min=33_628, - Network accessline 577
source_url="https://www.synapse.org/Synapse:syn52362400", - Network accessline 577
source_url="https://www.synapse.org/Synapse:syn52362400", - Network accessline 747
assert "https://www.synapse.org" in PAT_REQUIRED_MESSAGE - Network accessline 747
assert "https://www.synapse.org" in PAT_REQUIRED_MESSAGE - Access to secretsline 749
[Credential-related source omitted] - Access to secretsline 749
[Credential-related source omitted]
skills/ukb-ppp-region-fetch/ukb_ppp_region_fetch.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Access to secretsline 36
[Credential-related source omitted] - Access to secretsline 36
[Credential-related source omitted] - Access to secretsline 78
[Credential-related source omitted] - Access to secretsline 78
[Credential-related source omitted] - Network accessline 134
"""Records the UKB-PPP release + protein measurement metadata pinned per fetch (for the manifest). Mirrors `EQTLCatalogueRelease` so downstream - Network accessline 134
"""Records the UKB-PPP release + protein measurement metadata pinned per fetch (for the manifest). Mirrors `EQTLCatalogueRelease` so downstream - Network accessline 135
fetch (for the manifest). Mirrors `EQTLCatalogueRelease` so downstream - Network accessline 135
fetch (for the manifest). Mirrors `EQTLCatalogueRelease` so downstream - Network accessline 260
1. Register / sign in at https://www.synapse.org - Network accessline 260
1. Register / sign in at https://www.synapse.org - Network accessline 261
2. Accept the Synapse Terms of Use (one-time click-through). 3. Open Account Settings -> Personal Access Tokens (https://www.synapse.org/Profile:settings). - Network accessline 261
2. Accept the Synapse Terms of Use (one-time click-through). 3. Open Account Settings -> Personal Access Tokens (https://www.synapse.org/Profile:settings). - Network accessline 262
3. Open Account Settings -> Personal Access Tokens (https://www.synapse.org/Profile:settings). 4. Click "Create new token". Scopes: tick `view` and `download`. - Network accessline 262
3. Open Account Settings -> Personal Access Tokens (https://www.synapse.org/Profile:settings). 4. Click "Create new token". Scopes: tick `view` and `download`. - Network accessline 263
(https://www.synapse.org/Profile:settings). 4. Click "Create new token". Scopes: tick `view` and `download`. Copy the token immediately (Synapse shows it once). - Network accessline 263
(https://www.synapse.org/Profile:settings). 4. Click "Create new token". Scopes: tick `view` and `download`. Copy the token immediately (Synapse shows it once). - Access to secretsline 267
[Credential-related source omitted] - Access to secretsline 267
[Credential-related source omitted] - Network accessline 354
BASE_URL = "https://repo-prod.prod.sagebase.org/repo/v1" - Network accessline 354
BASE_URL = "https://repo-prod.prod.sagebase.org/repo/v1" - Network accessline 372
[Credential-related source omitted] - Network accessline 372
[Credential-related source omitted] - Network accessline 373
payload["nextPageToken"] = next_token resp = requests.post( url, json=payload, timeout=self.timeout_s, - Network accessline 373
payload["nextPageToken"] = next_token resp = requests.post( url, json=payload, timeout=self.timeout_s, - Network accessline 374
resp = requests.post( - Network accessline 374
resp = requests.post( - Access to secretsline 392
[Credential-related source omitted] - Access to secretsline 392
[Credential-related source omitted] - Access to secretsline 395
[Credential-related source omitted] - Access to secretsline 395
[Credential-related source omitted] - Access to secretsline 411
[Credential-related source omitted] - Access to secretsline 411
[Credential-related source omitted] - Access to secretsline 414
[Credential-related source omitted] - Access to secretsline 414
[Credential-related source omitted] - Network accessline 518
Two-path fetch (v1.3): - Network accessline 518
Two-path fetch (v1.3): - Access to secretsline 544
[Credential-related source omitted] - Access to secretsline 544
[Credential-related source omitted] - Access to secretsline 551
[Credential-related source omitted] - Access to secretsline 551
[Credential-related source omitted] - Network accessline 586
Resolution order: 1. Bundled slice (no auth) at `bundled_slices/<key>.json.gz`. 2. Live Synapse fetch (requires SYNAPSE_AUTH_TOKEN). - Network accessline 586
Resolution order: 1. Bundled slice (no auth) at `bundled_slices/<key>.json.gz`. 2. Live Synapse fetch (requires SYNAPSE_AUTH_TOKEN). - Network accessline 588
[Credential-related source omitted] - Network accessline 588
[Credential-related source omitted] - Access to secretsline 588
[Credential-related source omitted] - Access to secretsline 588
[Credential-related source omitted] - Network accessline 609
# Step 2: live Synapse fetch (or refuse if disabled). - Network accessline 609
# Step 2: live Synapse fetch (or refuse if disabled). - Network accessline 638
n_samples=n_max, synapse_id=rec["synapse_id"], source_url=f"https://www.synapse.org/Synapse:{rec['synapse_id']}", - Network accessline 638
n_samples=n_max, synapse_id=rec["synapse_id"], source_url=f"https://www.synapse.org/Synapse:{rec['synapse_id']}", - Network accessline 639
synapse_id=rec["synapse_id"], source_url=f"https://www.synapse.org/Synapse:{rec['synapse_id']}", n_samples_min=n_min, - Network accessline 639
synapse_id=rec["synapse_id"], source_url=f"https://www.synapse.org/Synapse:{rec['synapse_id']}", n_samples_min=n_min, - Network accessline 640
source_url=f"https://www.synapse.org/Synapse:{rec['synapse_id']}", - Network accessline 640
source_url=f"https://www.synapse.org/Synapse:{rec['synapse_id']}", - Access to secretsline 952
[Credential-related source omitted] - Access to secretsline 952
[Credential-related source omitted] - Network accessline 963
print( f"info: no bundled slice for {slice_path.name}; " "falling through to live Synapse fetch (PAT detected).", - Network accessline 963
print( f"info: no bundled slice for {slice_path.name}; " "falling through to live Synapse fetch (PAT detected).", - Network accessline 964
f"info: no bundled slice for {slice_path.name}; " "falling through to live Synapse fetch (PAT detected).", file=sys.stderr, - Network accessline 964
f"info: no bundled slice for {slice_path.name}; " "falling through to live Synapse fetch (PAT detected).", file=sys.stderr, - Network accessline 965
"falling through to live Synapse fetch (PAT detected).", - Network accessline 965
"falling through to live Synapse fetch (PAT detected).",
skills/variant-annotation/SKILL.md
- Network accessline 47
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 47
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 48
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 48
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 49
homepage: https://github.com/ClawBio/ClawBio - Network accessline 49
homepage: https://github.com/ClawBio/ClawBio - Network accessline 94
1. **Parse**: Read the VCF with `pysam.VariantFile` and emit one record per ALT allele. 2. **Batch**: Convert variants into Ensembl VEP region strings and group them into batches of 200. 3. **Annotate**: POST batches to `https://rest.ensemb - Network accessline 94
1. **Parse**: Read the VCF with `pysam.VariantFile` and emit one record per ALT allele. 2. **Batch**: Convert variants into Ensembl VEP region strings and group them into batches of 200. 3. **Annotate**: POST batches to `https://rest.ensemb - Network accessline 95
2. **Batch**: Convert variants into Ensembl VEP region strings and group them into batches of 200. 3. **Annotate**: POST batches to `https://rest.ensembl.org/vep/homo_sapiens/region` using GRCh38 as the default assembly. 4. **Normalise**: P - Network accessline 95
2. **Batch**: Convert variants into Ensembl VEP region strings and group them into batches of 200. 3. **Annotate**: POST batches to `https://rest.ensembl.org/vep/homo_sapiens/region` using GRCh38 as the default assembly. 4. **Normalise**: P - Network accessline 96
3. **Annotate**: POST batches to `https://rest.ensembl.org/vep/homo_sapiens/region` using GRCh38 as the default assembly. - Network accessline 96
3. **Annotate**: POST batches to `https://rest.ensembl.org/vep/homo_sapiens/region` using GRCh38 as the default assembly. - Network accessline 223
- [Ensembl Variant Effect Predictor](https://www.ensembl.org/info/docs/tools/vep/index.html) — functional consequence annotation - Network accessline 223
- [Ensembl Variant Effect Predictor](https://www.ensembl.org/info/docs/tools/vep/index.html) — functional consequence annotation - Network accessline 224
- [Ensembl REST API](https://rest.ensembl.org/) — batch VEP annotation endpoint used by the current backend - Network accessline 224
- [Ensembl REST API](https://rest.ensembl.org/) — batch VEP annotation endpoint used by the current backend - Network accessline 225
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) — clinical significance assertions - Network accessline 225
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/) — clinical significance assertions - Network accessline 226
- [gnomAD](https://gnomad.broadinstitute.org/) — population allele frequency reference data - Network accessline 226
- [gnomAD](https://gnomad.broadinstitute.org/) — population allele frequency reference data - Network accessline 227
- [VCF Specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf) — variant file format reference - Network accessline 227
- [VCF Specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf) — variant file format reference
skills/variant-annotation/tests/test_variant_annotation.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 109
def raise_for_status(self) -> None: if self.status_code >= 400: raise requests.HTTPError(f"status {self.status_code}") - Network accessline 109
def raise_for_status(self) -> None: if self.status_code >= 400: raise requests.HTTPError(f"status {self.status_code}") - Network accessline 111
raise requests.HTTPError(f"status {self.status_code}") - Network accessline 111
raise requests.HTTPError(f"status {self.status_code}")
skills/variant-annotation/variant_annotation.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 44
VEP_BASE_URL = "https://rest.ensembl.org" - Network accessline 44
VEP_BASE_URL = "https://rest.ensembl.org" - Network accessline 180
self.session = requests.Session() - Network accessline 180
self.session = requests.Session()
skills/vcf-annotator/SKILL.md
- Network accessline 7
requires: always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 7
requires: always: false homepage: https://github.com/ClawBio/ClawBio - Network accessline 8
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 8
always: false homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 9
homepage: https://github.com/ClawBio/ClawBio - Network accessline 9
homepage: https://github.com/ClawBio/ClawBio - Network accessline 174
1. **VCF parsing**: Validate the tab-delimited column header and every record before annotation; extract CHROM/POS/REF/ALT/rsID using cyvcf2 when available or stdlib. 2. **VEP**: `GET https://rest.ensembl.org/vep/human/hgvs/{hgvs}` — ret - Network accessline 174
1. **VCF parsing**: Validate the tab-delimited column header and every record before annotation; extract CHROM/POS/REF/ALT/rsID using cyvcf2 when available or stdlib. 2. **VEP**: `GET https://rest.ensembl.org/vep/human/hgvs/{hgvs}` — ret - Network accessline 175
annotation; extract CHROM/POS/REF/ALT/rsID using cyvcf2 when available or stdlib. 2. **VEP**: `GET https://rest.ensembl.org/vep/human/hgvs/{hgvs}` — returns gene symbol, consequence terms, impact, SIFT, PolyPhen - Network accessline 175
annotation; extract CHROM/POS/REF/ALT/rsID using cyvcf2 when available or stdlib. 2. **VEP**: `GET https://rest.ensembl.org/vep/human/hgvs/{hgvs}` — returns gene symbol, consequence terms, impact, SIFT, PolyPhen - Network accessline 176
2. **VEP**: `GET https://rest.ensembl.org/vep/human/hgvs/{hgvs}` — returns - Network accessline 176
2. **VEP**: `GET https://rest.ensembl.org/vep/human/hgvs/{hgvs}` — returns - Network accessline 177
gene symbol, consequence terms, impact, SIFT, PolyPhen 3. **ClinVar**: `esearch` on `clinvar` database with rsID term 4. **gnomAD**: GraphQL query to `https://gnomad.broadinstitute.org/api` with - Network accessline 177
gene symbol, consequence terms, impact, SIFT, PolyPhen 3. **ClinVar**: `esearch` on `clinvar` database with rsID term 4. **gnomAD**: GraphQL query to `https://gnomad.broadinstitute.org/api` with - Network accessline 178
3. **ClinVar**: `esearch` on `clinvar` database with rsID term 4. **gnomAD**: GraphQL query to `https://gnomad.broadinstitute.org/api` with variant ID format `{chrom}-{pos}-{ref}-{alt}` - Network accessline 178
3. **ClinVar**: `esearch` on `clinvar` database with rsID term 4. **gnomAD**: GraphQL query to `https://gnomad.broadinstitute.org/api` with variant ID format `{chrom}-{pos}-{ref}-{alt}` - Network accessline 179
4. **gnomAD**: GraphQL query to `https://gnomad.broadinstitute.org/api` with - Network accessline 179
4. **gnomAD**: GraphQL query to `https://gnomad.broadinstitute.org/api` with - Network accessline 294
- [Ensembl VEP](https://www.ensembl.org/vep); variant effect prediction - Network accessline 294
- [Ensembl VEP](https://www.ensembl.org/vep); variant effect prediction - Network accessline 295
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/); clinical variant classification - Network accessline 295
- [ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/); clinical variant classification - Network accessline 296
- [gnomAD](https://gnomad.broadinstitute.org/); population allele frequencies - Network accessline 296
- [gnomAD](https://gnomad.broadinstitute.org/); population allele frequencies - Network accessline 297
- [McLaren et al. 2016](https://doi.org/10.1186/s13059-016-0974-4); VEP paper - Network accessline 297
- [McLaren et al. 2016](https://doi.org/10.1186/s13059-016-0974-4); VEP paper
skills/vcf-annotator/tests/test_vcf_annotator.py
skills/vcf-annotator/vcf_annotator.py
- Executable scriptline 1
#!/usr/bin/env python3 - Executable scriptline 1
#!/usr/bin/env python3 - Network accessline 37
ENSEMBL_VEP_URL = "https://rest.ensembl.org/vep/human/hgvs" - Network accessline 37
ENSEMBL_VEP_URL = "https://rest.ensembl.org/vep/human/hgvs" - Network accessline 38
CLINVAR_API_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 38
CLINVAR_API_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi" - Network accessline 39
GNOMAD_API_URL = "https://gnomad.broadinstitute.org/api" - Network accessline 39
GNOMAD_API_URL = "https://gnomad.broadinstitute.org/api" - Access to secretsline 41
[Credential-related source omitted] - Access to secretsline 41
[Credential-related source omitted] - Network accessline 224
hgvs = f"{chrom}:g.{pos}{ref}>{alt}" url = f"https://rest.ensembl.org/vep/human/hgvs/{urllib.parse.quote(hgvs)}" - Network accessline 224
hgvs = f"{chrom}:g.{pos}{ref}>{alt}" url = f"https://rest.ensembl.org/vep/human/hgvs/{urllib.parse.quote(hgvs)}" - Network accessline 225
url = f"https://rest.ensembl.org/vep/human/hgvs/{urllib.parse.quote(hgvs)}" - Network accessline 225
url = f"https://rest.ensembl.org/vep/human/hgvs/{urllib.parse.quote(hgvs)}" - Network accessline 237
try: req = urllib.request.Request( - Network accessline 237
try: req = urllib.request.Request( - Network accessline 238
req = urllib.request.Request( - Network accessline 238
req = urllib.request.Request( - Network accessline 240
headers={"Content-Type": "application/json", "Accept": "application/json"}, ) with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 240
headers={"Content-Type": "application/json", "Accept": "application/json"}, ) with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 241
) with urllib.request.urlopen(req, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 241
) with urllib.request.urlopen(req, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 242
with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 242
with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 277
try: url = f"{CLINVAR_API_URL}?{params}" with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 277
try: url = f"{CLINVAR_API_URL}?{params}" with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 278
url = f"{CLINVAR_API_URL}?{params}" with urllib.request.urlopen(url, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 278
url = f"{CLINVAR_API_URL}?{params}" with urllib.request.urlopen(url, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 279
with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 279
with urllib.request.urlopen(url, timeout=10) as resp: - Network accessline 311
try: req = urllib.request.Request( - Network accessline 311
try: req = urllib.request.Request( - Network accessline 312
req = urllib.request.Request( - Network accessline 312
req = urllib.request.Request( - Network accessline 315
headers={"Content-Type": "application/json"}, ) with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 315
headers={"Content-Type": "application/json"}, ) with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 316
) with urllib.request.urlopen(req, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 316
) with urllib.request.urlopen(req, timeout=10) as resp: data = json.loads(resp.read().decode()) - Network accessline 317
with urllib.request.urlopen(req, timeout=10) as resp: - Network accessline 317
with urllib.request.urlopen(req, timeout=10) as resp:
skills/wes-clinical-report-en/SKILL.md
- Network accessline 38
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 38
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 39
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 39
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 40
homepage: https://github.com/ClawBio/ClawBio - Network accessline 40
homepage: https://github.com/ClawBio/ClawBio
skills/wes-clinical-report-en/tests/test_wes_clinical_report_en.py
skills/wes-clinical-report-en/wes_clinical_report_en.py
skills/wes-clinical-report-es/SKILL.md
- Network accessline 38
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 38
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 39
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 39
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 40
homepage: https://github.com/ClawBio/ClawBio - Network accessline 40
homepage: https://github.com/ClawBio/ClawBio
skills/wes-clinical-report-es/tests/test_wes_clinical_report_es.py
skills/wes-clinical-report-es/wes_clinical_report_es.py
skills/wgs-prs/SKILL.md
- Network accessline 17
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 17
always: false emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio - Network accessline 18
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 18
emoji: 🧬 homepage: https://github.com/ClawBio/ClawBio os: - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 19
homepage: https://github.com/ClawBio/ClawBio - Network accessline 23
install: - kind: url url: https://get.nextflow.io - Network accessline 23
install: - kind: url url: https://get.nextflow.io - Network accessline 24
- kind: url url: https://get.nextflow.io bins: - Network accessline 24
- kind: url url: https://get.nextflow.io bins: - Network accessline 25
url: https://get.nextflow.io - Network accessline 25
url: https://get.nextflow.io - Network accessline 26
bins: - nextflow note: curl -s https://get.nextflow.io | bash - Network accessline 26
bins: - nextflow note: curl -s https://get.nextflow.io | bash - Network accessline 27
- nextflow note: curl -s https://get.nextflow.io | bash - kind: conda - Network accessline 27
- nextflow note: curl -s https://get.nextflow.io | bash - kind: conda - Dangerous shell operationline 28
note: curl -s https://get.nextflow.io | bash - Dangerous shell operationline 28
note: curl -s https://get.nextflow.io | bash - Network accessline 28
note: curl -s https://get.nextflow.io | bash - Network accessline 28
note: curl -s https://get.nextflow.io | bash
skills/wgs-prs/tests/test_repro_bundle.py
skills/wgs-prs/tests/test_sarek.py
skills/wgs-prs/tests/test_vcf_qc.py
skills/wgs-prs/tests/test_wgs_prs.py
skills/wgs-prs/wgs_prs.py
skills/wgs-prs/wgs_prs_repro_bundle.py
skills/xena-tcga-gene-query/SKILL.md
- Network accessline 58
always: false emoji: "🦀" homepage: https://github.com/lishensuo/UCSCXenaToolsPy - Network accessline 58
always: false emoji: "🦀" homepage: https://github.com/lishensuo/UCSCXenaToolsPy - Network accessline 59
emoji: "🦀" homepage: https://github.com/lishensuo/UCSCXenaToolsPy os: - Network accessline 59
emoji: "🦀" homepage: https://github.com/lishensuo/UCSCXenaToolsPy os: - Network accessline 60
homepage: https://github.com/lishensuo/UCSCXenaToolsPy - Network accessline 60
homepage: https://github.com/lishensuo/UCSCXenaToolsPy - Network accessline 140
1. **Check API health** (prescriptive): try `curl http://biotree.top:38123/ucscxena/health` first (~0.2s). If unreachable, fall back to `https://ucscxenatoolspy.onrender.com/health` (may need ~30s cold start). If both are down, try `http:// - Network accessline 140
1. **Check API health** (prescriptive): try `curl http://biotree.top:38123/ucscxena/health` first (~0.2s). If unreachable, fall back to `https://ucscxenatoolspy.onrender.com/health` (may need ~30s cold start). If both are down, try `http:// - Network accessline 153
# Check health first (mandatory) curl http://biotree.top:38123/ucscxena/health || \ - Network accessline 153
# Check health first (mandatory) curl http://biotree.top:38123/ucscxena/health || \ - Network accessline 154
curl http://biotree.top:38123/ucscxena/health || \ - Network accessline 154
curl http://biotree.top:38123/ucscxena/health || \ - Network accessline 155
curl https://ucscxenatoolspy.onrender.com/health || \ - Network accessline 155
curl https://ucscxenatoolspy.onrender.com/health || \ - Network accessline 156
curl http://127.0.0.1:8765/health - Network accessline 156
curl http://127.0.0.1:8765/health - Network accessline 176
# Override base URL python skills/xena-tcga-gene-query/scripts/query_tcga_api.py diff-expr \ --gene TP53 --cancer LUAD --base-url http://biotree.top:38123/ucscxena/ - Network accessline 176
# Override base URL python skills/xena-tcga-gene-query/scripts/query_tcga_api.py diff-expr \ --gene TP53 --cancer LUAD --base-url http://biotree.top:38123/ucscxena/ - Network accessline 177
python skills/xena-tcga-gene-query/scripts/query_tcga_api.py diff-expr --gene TP53 --cancer LUAD --base-url http://biotree.top:38123/ucscxena/ - Network accessline 177
python skills/xena-tcga-gene-query/scripts/query_tcga_api.py diff-expr --gene TP53 --cancer LUAD --base-url http://biotree.top:38123/ucscxena/ - Network accessline 178
--gene TP53 --cancer LUAD --base-url http://biotree.top:38123/ucscxena/ - Network accessline 178
--gene TP53 --cancer LUAD --base-url http://biotree.top:38123/ucscxena/ - Network accessline 228
**Date**: 2026-07-06 **API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 228
**Date**: 2026-07-06 **API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 229
**API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 229
**API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 304
├── result.json # Machine-readable results (API responses) └── reproducibility/ ├── commands.sh # Exact curl commands to reproduce - Network accessline 304
├── result.json # Machine-readable results (API responses) └── reproducibility/ ├── commands.sh # Exact curl commands to reproduce - Network accessline 305
└── reproducibility/ ├── commands.sh # Exact curl commands to reproduce └── run.json # Run metadata (timestamps, base URL, API version) - Network accessline 305
└── reproducibility/ ├── commands.sh # Exact curl commands to reproduce └── run.json # Run metadata (timestamps, base URL, API version) - Network accessline 306
├── commands.sh # Exact curl commands to reproduce - Network accessline 306
├── commands.sh # Exact curl commands to reproduce - Network accessline 328
- **Author-hosted API service**: This skill sends gene symbols and cancer type codes to an author-hosted UCSCXenaToolsPy API endpoint (default: `http://biotree.top:38123/ucscxena/`, fallback: `https://ucscxenatoolspy.onrender.com`). The ser - Network accessline 328
- **Author-hosted API service**: This skill sends gene symbols and cancer type codes to an author-hosted UCSCXenaToolsPy API endpoint (default: `http://biotree.top:38123/ucscxena/`, fallback: `https://ucscxenatoolspy.onrender.com`). The ser - Network accessline 329
- **Disclaimer**: every `report.md` includes the standard ClawBio research-tool disclaimer. - **Audit trail**: every run writes `reproducibility/commands.sh` with the exact curl commands and `reproducibility/run.json` with metadata includin - Network accessline 329
- **Disclaimer**: every `report.md` includes the standard ClawBio research-tool disclaimer. - **Audit trail**: every run writes `reproducibility/commands.sh` with the exact curl commands and `reproducibility/run.json` with metadata includin - Network accessline 330
- **Audit trail**: every run writes `reproducibility/commands.sh` with the exact curl commands and `reproducibility/run.json` with metadata including the mode (demo vs live). - Network accessline 330
- **Audit trail**: every run writes `reproducibility/commands.sh` with the exact curl commands and `reproducibility/run.json` with metadata including the mode (demo vs live). - Network accessline 380
- [UCSC Xena](https://xena.ucsc.edu/) — TCGA expression data and clinical annotations. - Network accessline 380
- [UCSC Xena](https://xena.ucsc.edu/) — TCGA expression data and clinical annotations. - Network accessline 381
- [ucscxenatoolspy](https://github.com/lishensuo/UCSCXenaToolsPy) — Python toolkit and API for UCSC Xena data access. - Network accessline 381
- [ucscxenatoolspy](https://github.com/lishensuo/UCSCXenaToolsPy) — Python toolkit and API for UCSC Xena data access. - Network accessline 382
- [Toil recompute](https://toil.xenahubs.net/) — uniformly reprocessed TCGA/TARGET/GTEx expression compendium. - Network accessline 382
- [Toil recompute](https://toil.xenahubs.net/) — uniformly reprocessed TCGA/TARGET/GTEx expression compendium. - Network accessline 383
- [TCGA](https://www.cancer.gov/tcga) — The Cancer Genome Atlas, source of the underlying data. - Network accessline 383
- [TCGA](https://www.cancer.gov/tcga) — The Cancer Genome Atlas, source of the underlying data.
skills/xena-tcga-gene-query/examples/demo_output.md
- Network accessline 14
**Date**: 2026-07-06 12:00:00 UTC **API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 14
**Date**: 2026-07-06 12:00:00 UTC **API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 15
**API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 15
**API base URL**: http://biotree.top:38123/ucscxena/ - Network accessline 72
#!/bin/sh BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}" curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD" - Network accessline 72
#!/bin/sh BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}" curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD" - Network accessline 73
BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}" curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD" curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD" - Network accessline 73
BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}" curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD" curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD" - Network accessline 74
curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD" - Network accessline 74
curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD" - Network accessline 75
curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD" - Network accessline 75
curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD" - Network accessline 76
curl "${BASE_URL}/api/v1/survival?gene=TP53&cancer=LUAD" - Network accessline 76
curl "${BASE_URL}/api/v1/survival?gene=TP53&cancer=LUAD" - Network accessline 83
"skill": "xena-tcga-gene-query", "mode": "demo", "base_url": "http://biotree.top:38123/ucscxena/", - Network accessline 83
"skill": "xena-tcga-gene-query", "mode": "demo", "base_url": "http://biotree.top:38123/ucscxena/", - Network accessline 84
"mode": "demo", "base_url": "http://biotree.top:38123/ucscxena/", "timestamp_utc": "2026-07-06T12:00:00.000000+00:00", - Network accessline 84
"mode": "demo", "base_url": "http://biotree.top:38123/ucscxena/", "timestamp_utc": "2026-07-06T12:00:00.000000+00:00", - Network accessline 85
"base_url": "http://biotree.top:38123/ucscxena/", - Network accessline 85
"base_url": "http://biotree.top:38123/ucscxena/",
skills/xena-tcga-gene-query/references/api.md
skills/xena-tcga-gene-query/scripts/query_tcga_api.py
- Executable scriptline 1
#!/usr/bin/env python - Executable scriptline 1
#!/usr/bin/env python - Network accessline 25
DEFAULT_BASE_URL = os.getenv("UCSCXENA_API_BASE_URL", "http://biotree.top:38123/ucscxena/") - Network accessline 25
DEFAULT_BASE_URL = os.getenv("UCSCXENA_API_BASE_URL", "http://biotree.top:38123/ucscxena/") - Access to secretsline 26
[Credential-related source omitted] - Access to secretsline 26
[Credential-related source omitted] - Access to secretsline 54
[Credential-related source omitted] - Access to secretsline 54
[Credential-related source omitted] - Network accessline 59
[Credential-related source omitted] - Network accessline 59
[Credential-related source omitted] - Access to secretsline 59
[Credential-related source omitted] - Access to secretsline 59
[Credential-related source omitted] - Network accessline 60
[Credential-related source omitted] - Network accessline 60
[Credential-related source omitted] - Access to secretsline 60
[Credential-related source omitted] - Access to secretsline 60
[Credential-related source omitted] - Network accessline 61
req = urllib.request.Request(url, headers=headers, method="GET") - Network accessline 61
req = urllib.request.Request(url, headers=headers, method="GET") - Network accessline 62
try: with urllib.request.urlopen(req, timeout=timeout) as resp: text = resp.read().decode("utf-8") - Network accessline 62
try: with urllib.request.urlopen(req, timeout=timeout) as resp: text = resp.read().decode("utf-8") - Network accessline 63
with urllib.request.urlopen(req, timeout=timeout) as resp: - Network accessline 63
with urllib.request.urlopen(req, timeout=timeout) as resp: - Network accessline 477
"# Reproducibility commands for xena-tcga-gene-query (demo mode)\n" "# Replace BASE_URL with the actual API base URL for live queries.\n" 'BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}"\n' - Network accessline 477
"# Reproducibility commands for xena-tcga-gene-query (demo mode)\n" "# Replace BASE_URL with the actual API base URL for live queries.\n" 'BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}"\n' - Network accessline 478
"# Replace BASE_URL with the actual API base URL for live queries.\n" 'BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}"\n' 'curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD"\n' - Network accessline 478
"# Replace BASE_URL with the actual API base URL for live queries.\n" 'BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}"\n' 'curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD"\n' - Network accessline 479
'BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}"\n' 'curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD"\n' 'curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD"\n' - Network accessline 479
'BASE_URL="${UCSCXENA_API_BASE_URL:-http://biotree.top:38123/ucscxena/}"\n' 'curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD"\n' 'curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD"\n' - Network accessline 480
'curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD"\n' - Network accessline 480
'curl "${BASE_URL}/api/v1/diff-expr?gene=TP53&cancer=LUAD"\n' - Network accessline 481
'curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD"\n' - Network accessline 481
'curl "${BASE_URL}/api/v1/corr?gene1=TP53&gene2=EGFR&cancer=LUAD"\n' - Network accessline 482
'curl "${BASE_URL}/api/v1/survival?gene=TP53&cancer=LUAD"\n' - Network accessline 482
'curl "${BASE_URL}/api/v1/survival?gene=TP53&cancer=LUAD"\n' - Network accessline 486
task_display = task_key.replace("_", "-") if task_key == "cancers": curl_line = f'curl "${{BASE_URL}}/api/v1/cancers"\n' - Network accessline 486
task_display = task_key.replace("_", "-") if task_key == "cancers": curl_line = f'curl "${{BASE_URL}}/api/v1/cancers"\n' - Network accessline 487
if task_key == "cancers": curl_line = f'curl "${{BASE_URL}}/api/v1/cancers"\n' elif task_key == "diff_expr": - Network accessline 487
if task_key == "cancers": curl_line = f'curl "${{BASE_URL}}/api/v1/cancers"\n' elif task_key == "diff_expr": - Network accessline 488
curl_line = f'curl "${{BASE_URL}}/api/v1/cancers"\n' - Network accessline 488
curl_line = f'curl "${{BASE_URL}}/api/v1/cancers"\n' - Network accessline 489
elif task_key == "diff_expr": curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 489
elif task_key == "diff_expr": curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 490
curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' f'gene={results[task_key].get("gene","?")}&cancer={results[task_key].get("cancer","?")}"\n' - Network accessline 490
curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' f'gene={results[task_key].get("gene","?")}&cancer={results[task_key].get("cancer","?")}"\n' - Network accessline 491
f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 491
f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 494
elif task_key == "corr": curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 494
elif task_key == "corr": curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 495
curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' f'gene1={results[task_key].get("gene1","?")}&gene2={results[task_key].get("gene2","?")}' - Network accessline 495
curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' f'gene1={results[task_key].get("gene1","?")}&gene2={results[task_key].get("gene2","?")}' - Network accessline 496
f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 496
f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 500
else: curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 500
else: curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 501
curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' f'gene={results[task_key].get("gene","?")}&cancer={results[task_key].get("cancer","?")}"\n' - Network accessline 501
curl_line = ( f'curl "${{BASE_URL}}/api/v1/{task_display}?' f'gene={results[task_key].get("gene","?")}&cancer={results[task_key].get("cancer","?")}"\n' - Network accessline 502
f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Network accessline 502
f'curl "${{BASE_URL}}/api/v1/{task_display}?' - Access to secretsline 533
[Credential-related source omitted] - Access to secretsline 533
[Credential-related source omitted] - Access to secretsline 596
[Credential-related source omitted] - Access to secretsline 596
[Credential-related source omitted]
skills/xena-tcga-gene-query/tests/test_query.py
- Executable scriptline 1
Executable file - Executable scriptline 1
Executable file - Network accessline 272
"""Replacement for urllib.request.urlopen that returns synthetic data.""" - Network accessline 272
"""Replacement for urllib.request.urlopen that returns synthetic data.""" - Network accessline 290
with patch.object(query_tcga_api.urllib.request, "urlopen", _mock_urlopen): result = query_tcga_api._request( "http://biotree.top:38123/ucscxena/", - Network accessline 290
with patch.object(query_tcga_api.urllib.request, "urlopen", _mock_urlopen): result = query_tcga_api._request( "http://biotree.top:38123/ucscxena/", - Network accessline 291
result = query_tcga_api._request( "http://biotree.top:38123/ucscxena/", "/api/v1/diff-expr", - Network accessline 291
result = query_tcga_api._request( "http://biotree.top:38123/ucscxena/", "/api/v1/diff-expr", - Network accessline 292
"http://biotree.top:38123/ucscxena/", - Network accessline 292
"http://biotree.top:38123/ucscxena/",
How the signals fit together
Facts from a static read of the files at the pinned commit. They describe what the code does, not why.
Some files could not be read; the facts below still hold.
Declared and executed: 2 facts
- Contacts fonts.googleapis.com, which SKILL.md, the README and the plugin manifest do not mentionanalyze-fasta/analyze_fasta.py:505High confidence
- Contacts api.crossref.org, which SKILL.md, the README and the plugin manifest do not mentionarticle-data-fetcher/article_data_fetcher.py:44High confidence
Signal confidence: 498 facts
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
- Executable script in code of a file that runsclawbio.py:1High confidence
and 448 more
Only the first 500 facts are listed.
Works with
| Agent | Status | Evidence | Install to |
|---|---|---|---|
| Claude Code | Native | Manifest .claude-plugin/marketplace.json | .claude/skills/<skill-name>/ |
| Codex | Native | Manifest AGENTS.md | .agents/skills/<skill-name>/ |
| Cursor | Compatible | Standard SKILL.md skills/affinity-proteomics/SKILL.md | .cursor/skills/<skill-name>/ |
| Gemini CLI | Compatible | Standard SKILL.md skills/affinity-proteomics/SKILL.md | .gemini/skills/<skill-name>/ |
| GitHub Copilot | Compatible | Standard SKILL.md skills/affinity-proteomics/SKILL.md | .github/skills/<skill-name>/ |
| OpenCode | Compatible | Standard SKILL.md skills/affinity-proteomics/SKILL.md | .opencode/skills/<skill-name>/ |
- Native The repository ships a manifest, folder or frontmatter field for this agent.
- Compatible A standard SKILL.md that this agent can read.
- Unknown No evidence either way.
Derived automatically from paths, manifests and frontmatter. Not tested on each agent.
Add this badge to your README
It updates every night and links to this page.
[](https://hotskills.dev/skill/clawbio-clawbio/)