Pathway enrichment

Skill Alim430/bioresearch-agent/skills/biomedical/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.From its SKILL.md

Install

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

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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.

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.

Gives 0 of the 12 instructions most healthcare skills give in 211 tokens

Counted across 147 of the 152 authors here whose files we hold, read 2026-08-07

Export trial data to CSV formatin 11 of 147, across 2 files
Retrieve trial details using an NCT IDin 11 of 147, across 2 files
Split clinical datasets strictly by patientin 11 of 147, across 3 files
Use the ClinicalTrials.gov API v2in 10 of 147, across 1 file
Search trials by condition, drug, location, status or phasein 10 of 147, across 1 file
Use maximum page size for bulk data retrievalin 10 of 147, across 1 file
Extract and summarize key study informationin 10 of 147, across 1 file
Combine multiple filters for targeted searchesin 10 of 147, across 1 file
Print and review dataset statistics before modelingin 8 of 147, across 1 file
Start model development with simple baselinesin 8 of 147, across 1 file
Match preprocessing processors directly to data typesin 8 of 147, across 1 file
Monitor validation metrics for task type and class imbalancein 8 of 147, across 1 file

Said here and by no other author read

run the biomarker workflow for enrichment

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