zamushwani/biomedical-ai-skills

zamushwani/biomedical-ai-skills

Command Claude Code

Differential expression from a count matrix with DESeq2. Use when the user has bulk RNA-seq counts and wants DEGs, a volcano plot, or asks which genes differ between conditions.

zamushwani/biomedical-ai-skills

Command Claude Code

Spatial transcriptomics analysis: loading, spatial QC, spatially variable genes, deconvolution, domains. Use for Visium, Xenium, MERSCOPE, or CosMx data.

zamushwani/biomedical-ai-skills

Command Claude Code

Annotate and clinically interpret variants from a VCF. Use when the user has variant calls and wants functional annotation, ACMG classification, oncogenicity, or clinical tiers.

zamushwani/biomedical-ai-skills

Command Claude Code

Estimate immune cell composition from bulk RNA-seq. Use when the user asks about tumour microenvironment, immune infiltration, CIBERSORT/quanTIseq/xCell, or immune cell fractions.

zamushwani/biomedical-ai-skills

Command Claude Code

Fit dose-response curves and compute IC50/AUC. Use when the user has viability data across drug concentrations, or asks about IC50, EC50, or drug sensitivity.

zamushwani/biomedical-ai-skills

Command Claude Code

Kaplan-Meier curves and Cox models from clinical data. Use when the user asks about survival, prognosis, hazard ratios, or wants a KM plot.

zamushwani/biomedical-ai-skills

Command Claude Code

Quality control and filtering for single-cell RNA-seq. Use when the user has an h5ad/h5/10x matrix and wants QC, cell filtering, doublet detection, or asks why their cell count dropped.

zamushwani/biomedical-ai-skills

Command Claude Code

Query TCGA/GDC for projects, mutations, or clinical data. Use when the user asks for TCGA cohorts, mutation counts, or clinical variables from the Genomic Data Commons.

zamushwani/biomedical-ai-skills

Command Claude Code

Pathway enrichment on a ranked gene list (GSEA or ORA). Use when the user asks which pathways are enriched, wants GSEA/fgsea, or has DE results to interpret biologically.

zamushwani/biomedical-ai-skills

Command Claude Code

Tile a whole-slide image with tissue detection for downstream modelling. Use for .svs/.ndpi/.mrxs slides, OpenSlide, or when the user asks about patches, tiles, or WSI preprocessing.