bioresearch-pathway-enrichmentlisted

# BioResearch Agent — Pathway Enrichment Skill ## Capability Runs pathway / GO / KEGG enrichment. In the framework this is stage 2 of the `biomarker` workflow: it takes the differentially expressed genes and tests them against KEGG pathways and GO terms with a hypergeometric test. ## Run ```bash bioresearch run biomarker --disease "Parkinson's disease" ``` (Invokes the biomarker workflow; enrichment is produced in stage 2.) ## Outputs (in `outputs/biomarker/`) - `biomarker_pathway_enrichment.csv` — enriched pathways / GO terms with p-values ## Note There is no standalone `pathway-enrichment` CLI command — enrichment is computed inside the `biomarker` workflow. This skill is a focused entry point that triggers that workflow when the user's intent is specifically pathway / GO / KEGG enrichment. It adds **no statistics of its own**.