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Skill
scvelo
K-Dense-AI/scientific-agent-skills · skills/scvelo
Performs RNA velocity analysis with scVelo from spliced and unspliced single-cell RNA counts. Fits deterministic or dynamical models, examines gene phase portraits, builds velocity graphs, estimates relative latent time, and ranks velocity-associated genes. Use for directional trajectory hypotheses and kinetic-model diagnostics alongside Scanpy; velocity alone does not establish cell fate or causal drivers.
Repository stars: 56,400 · Incomplete scan
Skill
markitdown
K-Dense-AI/scientific-agent-skills · skills/markitdown
Converts heterogeneous documents and selected URIs to Markdown with Microsoft MarkItDown for text analysis, search, and LLM/RAG ingestion. Covers safe local conversion, streams, Office/PDF/data formats, batch workflows, plugins, vision OCR, Azure extraction, and the official MCP server.
Repository stars: 56,400 · Incomplete scan
Skill
exploratory-data-analysis
K-Dense-AI/scientific-agent-skills · skills/exploratory-data-analysis
Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5, FASTA/FASTQ, and basic image metadata inspection; missingness/leakage audits; outlier and transformation sensitivity; and rigorous EDA report scaffolds. Other domain formats are reference-only and unknown formats fail closed.
Repository stars: 56,400 · Incomplete scan
Skill
pathway-enrichment
K-Dense-AI/scientific-agent-skills · skills/pathway-enrichment
Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".
Repository stars: 56,400 · Incomplete scan
Skill
what-if-oracle
K-Dense-AI/scientific-agent-skills · skills/what-if-oracle
Supports structured what-if scenario analysis for research planning, experimental contingencies, and scientific project decisions. Explores favorable, reference, adverse, wild-card, contrarian, and second-order scenarios with explicit assumptions, evidence, and decision triggers. Use to stress-test a research plan under uncertainty; scenario narratives do not estimate causal effects or calibrated forecast probabilities.
Repository stars: 56,400 · Incomplete scan
Skill
geniml
K-Dense-AI/scientific-agent-skills · skills/geniml
Supports audited local Geniml genomic-interval workflows: validate BED and universe contracts, plan Region2Vec or scEmbed runs, inspect model/tokenizer compatibility, and assess consensus universes.
Repository stars: 56,400 · Incomplete scan
Skill
rdkit
K-Dense-AI/scientific-agent-skills · skills/rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows with simpler interface, use datamol (wrapper around RDKit). Use rdkit for advanced control, custom sanitization, specialized algorithms.
Repository stars: 56,400 · Incomplete scan
Skill
polars-bio
K-Dense-AI/scientific-agent-skills · skills/polars-bio
Performs genomic interval overlap, nearest, merge, coverage, complement and subtraction on Polars DataFrames, and reads or writes BED, VCF, BCF, BAM, CRAM, GFF, GTF, FASTA and FASTQ data. Use for coordinate-aware genomic joins, read-depth analysis, lazy bioinformatics I/O, SQL queries or migration from bioframe.
Repository stars: 56,400 · Incomplete scan
Skill
pathogen-variant-surveillance
K-Dense-AI/scientific-agent-skills · skills/pathogen-variant-surveillance
Queries public GenSpectrum LAPIS data for pathogen genomic surveillance, current lineage nomenclature, weekly sequence proportions, reporting delays, and descriptive mutation frequencies. Use for variant surveillance, Pango lineage validation, dominant submitted lineages, Nextclade assignment provenance, SARS-CoV-2, influenza/H5N1 clades, RSV, mpox, measles, dengue, or LAPIS queries. Distinguishes sequence prevalence from infection prevalence, clades from genotypes, missing calls from reference matches, and sampling changes from biological growth advantage.
Repository stars: 56,400 · Incomplete scan
Skill
scvi-tools
K-Dense-AI/scientific-agent-skills · skills/scvi-tools
Fits probabilistic models for single-cell omics, including scVI batch integration, scANVI annotation, totalVI CITE-seq, MultiVI RNA/ATAC integration, and posterior differential expression. Use for generative modeling, reference mapping, multimodal analysis, or model-based uncertainty; use scanpy for standard preprocessing and exploratory analysis.
Repository stars: 56,400 · Incomplete scan
Skill
labarchive-integration
K-Dense-AI/scientific-agent-skills · skills/labarchive-integration
Integrates with the official LabArchives ELN REST-like API and Inventory API v1. Supports regional endpoint selection, signed-request construction, user authorization and UID flows, local LA container validation, and verified LabArchives integration workflows.
Repository stars: 56,400 · Incomplete scan
Skill
gget
K-Dense-AI/scientific-agent-skills · skills/gget
Queries 20+ bioinformatics resources through CLI/Python. Supports quick lookups of gene info, BLAST/BLAT, viral sequence downloads, PDB/mmCIF structures, G2P residue annotations, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
Repository stars: 56,400 · Incomplete scan
Skill
genomic-intelligence
K-Dense-AI/scientific-agent-skills · skills/genomic-intelligence
Predicts regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights. Six tasks over a REST API and a hosted MCP server (keyless public demo): promoter regions, splice donor/acceptor sites, enhancer activity, chromatin state, sequence-to-expression (log TPM), and de-novo gene annotation, plus a composite find-genes-then-predict-expression workflow. Use when the user has a gene symbol, a genomic region, or a DNA/FASTA sequence and wants any of these predictions, mentions Genomic Intelligence, genomicintelligence.ai, api.genomicintelligence.ai, or mcp.genomicintelligence.ai.
Repository stars: 56,400 · Incomplete scan
Skill
scikit-learn
K-Dense-AI/scientific-agent-skills · skills/scikit-learn
Supports machine learning in Python with scikit-learn. Applies when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
Repository stars: 56,400 · Incomplete scan
Skill
scientific-writing
K-Dense-AI/scientific-agent-skills · skills/scientific-writing
Drafts, revises, and audits scientific manuscripts or reports with explicit evidence provenance, reporting-guideline coverage, authorship accountability, confidentiality controls, and local consistency checks. Use for manuscript sections, references, declarations, tables, figures, or submission preparation when scientific accuracy and traceability matter.
Repository stars: 56,400 · Incomplete scan
Skill
pybamm
K-Dense-AI/scientific-agent-skills · skills/pybamm
Simulates lithium-ion battery charge, discharge and rest experiments with PyBaMM, records parameter-set provenance, checks mesh and solver sensitivity, and compares predicted voltage curves with measured cycling data. Use for SPM or DFN electrochemical battery modeling, C-rate protocols, voltage cutoffs, parameter studies and numerical validation of battery simulations.
Repository stars: 56,400 · Incomplete scan
Skill
13c-metabolic-flux
K-Dense-AI/scientific-agent-skills · skills/13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps, mfapy isotope simulation, constrained multistart fitting, and flux-profile diagnostics. Use for 13C-MFA, carbon tracing, mass isotopomer distributions (MDVs/MIDs), positional isotopomers, parallel tracer experiments, and determining whether labeling data constrain a pathway flux. Distinguishes measured-label inference from COBRA flux balance analysis and flags experiments requiring nonstationary MFA.
Repository stars: 56,400 · Incomplete scan
Skill
datamol
K-Dense-AI/scientific-agent-skills · skills/datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
Repository stars: 56,400 · Incomplete scan
Skill
benchling-integration
K-Dense-AI/scientific-agent-skills · skills/benchling-integration
Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.
Repository stars: 56,400 · Incomplete scan
Skill
esm
K-Dense-AI/scientific-agent-skills · skills/esm
Uses the Biohub esm Python SDK for ESM3 protein generation, ESMC embeddings, and ESMFold2 all-atom folding. Applies to local model inference and Biohub hosted clients, including former Forge workflows; distinguishes the separate legacy fair-esm distribution.
Repository stars: 56,400 · Incomplete scan
Skill
mageck
K-Dense-AI/scientific-agent-skills · skills/mageck
Analyzes pooled CRISPR screen FASTQ reads and guide-count matrices with MAGeCK, validates guide libraries and contrasts, measures replicate and library QC, and produces gene hit rankings with effect sizes and FDR. Use for new knockout, CRISPRi, or CRISPRa screen analysis, enrichment or depletion contrasts, and MAGeCK count/test workflows; existing public dependency-score lookup belongs to DepMap.
Repository stars: 56,400 · Incomplete scan
Skill
seaborn
K-Dense-AI/scientific-agent-skills · skills/seaborn
Creates Seaborn statistical visualizations with pandas integration for distributions, relationships, categorical comparisons, regression displays, pair plots, and heatmaps. Supports function and objects interfaces with explicit aggregation, uncertainty, and missing-data handling. Best suited to static exploratory plots; plotly covers interactive figures and scientific-visualization covers publication styling.
Repository stars: 56,400 · Incomplete scan
Skill
umap-learn
K-Dense-AI/scientific-agent-skills · skills/umap-learn
Applies UMAP-learn to nonlinear dimensionality reduction, 2D/3D embeddings, clustering preprocessing, supervised or semi-supervised UMAP, DensMAP, AlignedUMAP, and Parametric UMAP workflows.
Repository stars: 56,400 · Incomplete scan
Skill
scientific-brainstorming
K-Dense-AI/scientific-agent-skills · skills/scientific-brainstorming
Facilitates evidence-aware scientific ideation with independent generation, structured discussion, explicit assumptions, transparent evaluation, adversarial review, and decision logs. Use for early-stage research brainstorming or prioritizing candidate directions; hand off empirical validation, study design, ethics or regulatory review, and clinical questions to appropriate experts or skills.
Repository stars: 56,400 · Incomplete scan
Skill
adaptyv
K-Dense-AI/scientific-agent-skills · skills/adaptyv
Uses the Adaptyv Bio Foundry API and Python SDK to design protein characterization experiments, estimate costs, submit sequences, monitor laboratory progress, and retrieve results. Applies to Adaptyv Foundry, its target catalog, binding screening and affinity assays, thermostability, expression, fluorescence, epitope binning, and enzyme activity workflows, including code using adaptyv or FoundryClient.
Repository stars: 56,400 · Incomplete scan
Skill
sympy
K-Dense-AI/scientific-agent-skills · skills/sympy
Performs exact symbolic mathematics with SymPy for algebra, calculus, equation solving, symbolic linear algebra, physics, and lambdify or LaTeX code generation. Use when a task needs symbolic results, explicit assumptions, or exact arithmetic; use NumPy or SciPy for purely numerical workloads.
Repository stars: 56,400 · Incomplete scan
Skill
imaging-data-commons
K-Dense-AI/scientific-agent-skills · skills/imaging-data-commons
Queries and downloads public cancer imaging data from NCI Imaging Data Commons. Supports IDC collection discovery, DICOM access, radiology (CT, MR, PET) and pathology AI datasets, metadata SQL, visualization, licensing, and citations. Uses public metadata and download routes without authentication; optional BigQuery and Google Healthcare routes require Google credentials.
Repository stars: 56,400 · Incomplete scan
Skill
depmap
K-Dense-AI/scientific-agent-skills · skills/depmap
Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers, and PRISM drug sensitivity. Supports cancer-selective dependency, co-essentiality, and candidate synthetic-lethality analyses with release-aware identifiers and statistical checks.
Repository stars: 56,400 · Incomplete scan
Skill
pyhealth
K-Dense-AI/scientific-agent-skills · skills/pyhealth
Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for PyHealth dataset loading, MIMIC-III/IV, eICU or OMOP prediction tasks, patient-level evaluation, mortality/readmission/length-of-stay modeling, medication recommendation, sleep staging, Trainer checkpoints, and ICD/ATC/NDC/RxNorm mapping.
Repository stars: 56,400 · Incomplete scan
Skill
pyopenms
K-Dense-AI/scientific-agent-skills · skills/pyopenms
Processes mass spectrometry data with pyOpenMS. Supports proteomics and metabolomics workflows—feature detection, peptide/protein identification, label-free quantification, adduct/accurate-mass annotation, and complex LC-MS/MS pipelines. Supports extensive file formats and algorithms. For simple spectral comparison and small-molecule library matching use matchms.
Repository stars: 56,400 · Incomplete scan
Skill
pytdc
K-Dense-AI/scientific-agent-skills · skills/pytdc
Provides Therapeutics Data Commons workflows through PyTDC for registry discovery, dataset access, task-aware splits, evaluator metrics, benchmark groups, and bounded molecular-oracle scoring. Use when working with TDC therapeutic ML datasets or benchmarks.
Repository stars: 56,400 · Incomplete scan
Skill
shap
K-Dense-AI/scientific-agent-skills · skills/shap
Explain and audit machine-learning predictions with SHAP. Use for selecting SHAP explainers and maskers, computing and validating feature attributions, handling multi-output explanations, and producing local or global SHAP visualizations.
Repository stars: 56,400 · Incomplete scan
Skill
clinical-decision-support
K-Dense-AI/scientific-agent-skills · skills/clinical-decision-support
Prepares and validates research-only clinical decision-support evaluation, evidence-profile, cohort, survival, biomarker/model, privacy, and governance artifacts. Supports aggregate or synthetic research documentation and traceability, excluding patient care and live clinical operation.
Repository stars: 56,400 · Incomplete scan
Skill
cellprofiler
K-Dense-AI/scientific-agent-skills · skills/cellprofiler
Runs reproducible CellProfiler microscopy pipelines for nuclear segmentation, cell counts, and per-object fluorescence measurements. Supports image/channel manifests, headless batch execution, segmentation overlays, and measurement QC for 2D fluorescence assays.
Repository stars: 56,400 · Incomplete scan
Skill
opentrons-integration
K-Dense-AI/scientific-agent-skills · skills/opentrons-integration
Authors, reviews, migrates, simulates, and troubleshoots official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid handling, deck and labware setup, pipettes, modules, runtime parameters, liquid classes, and Opentrons App analysis. Use pylabrobot instead when one workflow must support multiple robot vendors.
Repository stars: 56,400 · Incomplete scan
Skill
paperzilla
K-Dense-AI/scientific-agent-skills · skills/paperzilla
Reads projects, searches project feeds, and retrieves recommendations and canonical papers in Paperzilla through the pz CLI. Supports recent recommendations, paper details, markdown-based summaries, recommendation feedback, JSON export, and Atom feed URLs.
Repository stars: 56,400 · Incomplete scan
Skill
hugging-science
K-Dense-AI/scientific-agent-skills · skills/hugging-science
Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific ML resources in biology, chemistry, genomics, materials, climate, physics, astronomy, medicine, mathematics, protein design, single-cell analysis, or PDE modeling, and when checking their actual datasets, Transformers, native-runtime, Inference Providers, or Gradio interfaces.
Repository stars: 56,400 · Incomplete scan
Skill
open-notebook
K-Dense-AI/scientific-agent-skills · skills/open-notebook
Organizes research with the self-hosted Open Notebook alternative to NotebookLM. Supports source ingestion (PDFs, web pages, audio, video, and Office documents), cited document chat, text and vector search, notes, custom transformations, and multi-speaker podcasts. Use when automating Open Notebook through its REST API or configuring its local or cloud AI providers, including OpenAI, Anthropic, Google, Ollama, Groq, and Mistral.
Repository stars: 56,400 · Incomplete scan
Skill
venue-templates
K-Dense-AI/scientific-agent-skills · skills/venue-templates
Prepares journal manuscripts, conference papers, research posters, and grant documents using venue-specific formatting guidance and bundled LaTeX scaffolds. Supports selecting an official template, checking current page or anonymity rules, adapting academic writing to a venue, or inspecting a submission PDF.
Repository stars: 56,400 · Incomplete scan
Skill
flowkit
K-Dense-AI/scientific-agent-skills · skills/flowkit
Analyzes flow cytometry data with FlowKit, including spillover compensation, logicle and biexponential transforms, hierarchical gating, GatingML strategies, and supported FlowJo 10 workspaces. Use for reproducible gate counts, population percentages, gated fluorescence summaries, or reproducing a FlowJo analysis in Python. For FCS metadata inspection or file-format repair alone, use FlowIO.
Repository stars: 56,400 · Incomplete scan
Skill
stable-baselines3
K-Dense-AI/scientific-agent-skills · skills/stable-baselines3
Trains and evaluates single-agent reinforcement learning with Stable Baselines3 (PPO, SAC, DQN, TD3, DDPG, A2C), Gymnasium custom environments, vectorized rollouts, callbacks, and checkpoint normalization. Applies to reproducible RL experiments, continuous control, discrete actions, and SB3-Contrib recurrent or masked policies.
Repository stars: 56,400 · Incomplete scan
Skill
paperclip
K-Dense-AI/scientific-agent-skills · skills/paperclip
Searches and reads biomedical papers, FDA/PMDA/EMA documents, clinical trials, and protein records with the GXL Paperclip CLI and Python SDK. Supports source-scoped search, full-text grep, metadata SQL, map/reduce extraction, figure analysis, optional repositories and claim verification, and line-pinned citations. Use when a task names GXL paperclip, asks to install or authenticate it, or requests literature retrieval and evidence extraction through Paperclip.
Repository stars: 56,400 · Incomplete scan
Skill
medchem
K-Dense-AI/scientific-agent-skills · skills/medchem
Applies medicinal chemistry filters for compound triage, using drug-likeness rules (Lipinski, Veber, CNS), structural alert catalogs (PAINS, NIBR, ChEMBL), complexity metrics, and the medchem query language for library filtering.
Repository stars: 56,400 · Incomplete scan
Skill
geopandas
K-Dense-AI/scientific-agent-skills · skills/geopandas
Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.
Repository stars: 56,400 · Incomplete scan
Skill
statistical-power
K-Dense-AI/scientific-agent-skills · skills/statistical-power
Calculates sample sizes and statistical power for study planning. Applies when someone asks "how many subjects/samples/replicates do I need", wants an a priori power analysis, a minimum detectable effect (MDE), a power curve, or needs to justify a sample size for a grant, IRB protocol, or pre-registration. Covers closed-form power for t-tests, ANOVA, proportions, correlations, chi-square, and regression, plus simulation-based (Monte Carlo) power for complex designs — logistic/Poisson regression, mixed models, cluster-randomized trials, survival, and interactions. Also handles requests that only mention an effect size, alpha, or "80% power" without saying "power analysis" explicitly. For laying out the study (randomization, blocking, factorial/DOE, crossover, sequential designs) use experimental-design; for analyzing data already collected and reporting it use statistical-analysis.
Repository stars: 56,400 · Incomplete scan
Skill
neurokit2
K-Dense-AI/scientific-agent-skills · skills/neurokit2
Builds and audits reproducible NeuroKit2 research workflows for physiological time-series preprocessing, event/interval analysis, multimodal alignment, variability, and complexity. Use when code imports neurokit2 or needs its current APIs, schemas, and method-aware validation—not for diagnosis or device validation.
Repository stars: 56,400 · Incomplete scan
Skill
markdown-mermaid-writing
K-Dense-AI/scientific-agent-skills · skills/markdown-mermaid-writing
Writes scientific Markdown documentation and Mermaid diagrams for workflows, relationships, timelines, and schemas. Provides syntax references, document templates, accessibility guidance, and version-aware rendering checks. Use when a user requests Markdown, Mermaid, or a text-based structural diagram; quantitative scientific figures require suitable plotting tools.
Repository stars: 56,400 · Incomplete scan
Skill
deeptutor/capabilities/creator/prompts/en
HKUDS/DeepTutor · deeptutor/capabilities/creator/prompts/en
Repository stars: 56,364 · Incomplete scan
Skill
xlsx
HKUDS/DeepTutor · deeptutor/skills/builtin/xlsx
Read, create, or edit Excel spreadsheets (.xlsx/.xlsm) — sheet data, formulas, styles, charts, multi-sheet workbooks — and bulk .csv/.tsv tables; use whenever a spreadsheet is the input or the deliverable (extract/analyze data, add columns/formulas/formatting/charts, clean messy tables, build from scratch), but not for Google Sheets API or Word/PDF/script outputs.
Repository stars: 56,364 · Incomplete scan
Skill
deeptutor-cli
HKUDS/DeepTutor · Root skill
Configure, manage, and use DeepTutor through its CLI, including capabilities, knowledge bases, partners, memory, sessions, notebooks, providers, skills, and the server or Web app.
Repository stars: 56,364 · Incomplete scan
Automated signals, not a guarantee. How the checks work.
