Tooluniverse Gene Enrichment

Runs GO, KEGG, and Reactome pathway enrichment on gene lists via gseapy or clusterProfiler. Built to solve the two big headaches in enrichment analysis: the canonical notebooks always use pre-computed results that you can't reproduce exactly (because the DEG filter or library snapshot was slightly different), and top hits constantly tie at the same adjusted p-value with no obvious winner. Ships three CLI scripts that handle tie-breaking deterministically, track candidate term ranks through simplify operations, and screen multiple conditions at once. The compute-first philosophy is solid: it immediately checks for executed notebooks and pre-computed CSVs before re-running anything, which saves you from chasing phantom discrepancies when the published answer is already sitting in the data folder.

Install to Claude Code

npx -y skills add mims-harvard/tooluniverse --skill tooluniverse-gene-enrichment --agent claude-code