pathway-enrichment

SUMMARY

What it does

This skill performs pathway and gene-set enrichment analysis on gene lists or ranked gene data, covering over-representation analysis (ORA), ranked Gene Set Enrichment Analysis (GSEA), and single-sample scoring (ssGSEA/GSVA). It supports multiple gene-set databases and tools including gseapy, g:Profiler, Enrichr, MSigDB, GO, KEGG, Reactome, and WikiPathways. The skill includes guidance on gene-ID mapping, background universe selection, multiple-testing correction, redundancy reduction, visualization, and interpretation. It is intended for use with gene lists from differential expression, CRISPR screens, cluster markers, or proteomics studies.