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
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.