Bioresearch Pathway Enrichment
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.
Install
$ agentstack add skill-alim430-bioresearch-agent-pathway-enrichment ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
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Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
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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.
Source & license
This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.
- Author: Alim430
- Source: Alim430/bioresearch-agent
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.