Pathway enrichment

Skill Alim430/bioresearch-agent/skills/biomedical/pathway-enrichment

Executable biomedical workflows for AI assistants — literature analysis, biomarker discovery, and Mendelian randomization through reproducible agent skills.

Install

npx -y skills add Alim430/bioresearch-agent --skill pathway-enrichment

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Run pathway enrichment (hypergeometric KEGG / GO) via the BioResearch Agent biomarker workflow, which performs enrichment after differential expression. Use when the user asks for pathway, GO, or KEGG enrichment analysis for a disease or a gene set.

SKILL.md

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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.