Biomedical Skills
SKILL.md files for cancer bioinformatics. Drop one into your project and your AI coding agent handles TCGA data, normalization, and statistics correctly.
Works with Claude Code · Cursor · Codex CLI · Gemini CLI
Skills
| Skill | Description | Tests |
|---|---|---|
cancer-multiomics |
Multi-omics analysis for TCGA/GEO — expression (DESeq2), mutation (maftools), CNV (GISTIC2), methylation (minfi, DMRcate) | TCGA-LUAD |
immune-deconvolution |
Tumor microenvironment estimation via immunedeconv — quanTIseq, EPIC, CIBERSORT, xCell, MCP-counter, TIMER, ESTIMATE, tumor purity correction | TCGA-BRCA |
survival-analysis |
Time-to-event analysis — Kaplan-Meier (ggsurvfit), Cox PH (survival), competing risks (tidycmprsk), RMST (survRM2), optimal cutpoints, forest plots | TCGA-GBM |
single-cell-atlas |
Full scRNA-seq pipeline — QC, doublet detection, normalization, batch integration (Harmony, scVI), Leiden clustering, annotation (CellTypist), pseudobulk DE, trajectory (scVelo, Monocle3), cell communication (CellChat, LIANA), TF activity (decoupleR). Seurat v5 + scanpy | PBMC 3k |
spatial-transcriptomics |
Visium, Visium HD, Xenium, MERSCOPE, CosMx — loading (spatialdata, VisiumIO), spatially local QC (SpotSweeper), spatially variable genes (squidpy, nnSVG), deconvolution (RCTD, cell2location), domains (BANKSY, CellCharter), communication (LIANA+) | Visium mouse brain |
foundation-models |
scGPT, Geneformer, UCE, TranscriptFormer, Nicheformer, Tahoe-x1 — zero-shot embeddings, fine-tuning for annotation, in-silico perturbation, and the benchmark evidence for when a linear baseline wins instead | PBMC 3k |
variant-annotation |
VCF normalization and filtering (bcftools), functional annotation (VEP, SnpEff, ANNOVAR), germline classification (ACMG/AMP with ClinGen refinements), somatic oncogenicity (ClinGen/CGC/VICC) and clinical tiers (AMP/ASCO/CAP, OncoKB, CIViC), TMB, MSI (msisensor-pro), neoantigen prediction (pVACtools) | TCGA-LAML |
meta-analysis |
Systematic review from protocol to synthesis — PROSPERO pre-specification, PICO search construction (MeSH, Emtree, Cochrane CHSSS), deduplication (synthesisr), two-reviewer screening with kappa, PRISMA 2020 flow diagrams, data extraction, risk of bias (RoB 2, ROBINS-I, ROBINS-E, robvis), pooling with metafor (REML, Knapp-Hartung, prediction intervals), subgroup analysis, meta-regression, small-study effects, network meta-analysis (netmeta, transitivity, inconsistency, rankings) and GRADE/CINeMA certainty | BCG |
Quick start
pip install biomedical-ai-skills
From your project directory:
biomedical-skills list # what's available
biomedical-skills install spatial-transcriptomics # -> .claude/skills/
biomedical-skills install --all # everything
biomedical-skills install cancer-multiomics --target .cursor/skills
No dependencies, so it installs in a couple of seconds.
Or skip the package and copy the files directly:
git clone https://github.com/zamushwani/biomedical-ai-skills.git
mkdir -p your-project/.claude/skills/cancer-multiomics
cp skills/cancer-multiomics/SKILL.md your-project/.claude/skills/cancer-multiomics/
What's a SKILL.md?
A file that gives AI coding agents domain knowledge for a specific field. The agent reads it before generating code and follows tested protocols instead of guessing at parameters.
Without a skill: agent runs DESeq2 without pre-filtering, skips lfcShrink(), uses wrong contrast syntax.
With a skill: agent pre-filters low-count genes, applies apeglm shrinkage, handles TCGA barcodes correctly.
Contributing
See CONTRIBUTING.md and SECURITY.md.
License
1 maintainer
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