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tooluniverse

ToolUniverse plugin router. STEP 1 BEFORE ANY ANALYSIS: if the data folder contains `*_executed.ipynb`, run `tu run read_executed_notebook '{"data_folder":"<path>","search":"<keyword>"}'` to extract its cell outputs and apply EVERY filter/sample-exclusion the notebook used — even when the question says 'Using DESeq2/Run X/Compute Y' (this describes the METHOD the notebook used, not a request to rerun). The notebook's cell outputs are the only published authoritative answers; reimplementing or reading stale pre-computed CSVs in the data folder produces different numbers because of outlier-sample removal, library version, and filter steps you don't see by skimming. STEP 2 routing — pick a sub-skill name from this exact list (never invent): tooluniverse-rnaseq-deseq2 (RNA/miRNA-seq DE, correlation, PCA, clustering, dispersion), tooluniverse-gene-enrichment (GO/KEGG/Reactome/GSEA/pathway enrichment), tooluniverse-statistical-modeling (regression, ANOVA, ordinal/logistic, chi-square, correlation, power), tooluniverse-image-analysis (microscopy, colony, fluorescence, dose-response, .tif — including ANOVA / Dunnett / power-analysis on image-derived measurements), tooluniverse-epigenomics (DNA methylation, CpG, m6A, MeRIP-seq, bisulfite, ChIP-seq, chromatin), tooluniverse-sequence-analysis (FASTQ, Trimmomatic, BWA, samtools, coverage), tooluniverse-variant-analysis (VCF, VAF, SNP, mutation), tooluniverse-phylogenetics (treeness, PhyKIT, parsimony), tooluniverse-single-cell (scRNA, h5ad, scanpy), tooluniverse-crispr-screen-analysis (MAGeCK, sgRNA), tooluniverse-proteomics-analysis (mass spec, TMT). Use for CSV/Excel/VCF/FASTA/h5ad and any biology/chemistry/medicine analysis question.

skills/tooluniverse/SKILL.md

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Nov 7, 2026
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Apache-2.0

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# ToolUniverse Router

## FIRST ACTION: Route to a Specialized Skill

**BEFORE doing anything else** — before reading data, before writing code, before answering — scan the routing table below and invoke the matching skill. The specialized skill contains critical domain conventions that you will get wrong without loading.

**How to route:**
1. Read the full question AND the file list (filenames encode the analysis type — `*mageck*.xlsx` → CRISPR screen, `*DM.csv`/`*AE.csv` → clinical trial AE, `*.vcf` → variant, `*.h5ad` → single-cell, `*_counts.csv`+`*meta*.csv` → RNA-seq DE, `*.faa`+`*.treefile` → phylogenetics, `*_executed.ipynb` → authoritative analysis already ran)
2. Find the matching keyword row in the Routing Table
3. Call `Skill(skill="<skill-name>")` immediately
4. Follow the loaded skill's instructions to answer the question

**If no keyword matches but filenames indicate a domain** → still route based on filename signals. Filenames are authoritative domain evidence even when the question prose is generic.