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Bioresearch Pathway Enrichment

skill-alim430-bioresearch-agent-pathway-enrichment · by Alim430

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.

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Install

$ agentstack add skill-alim430-bioresearch-agent-pathway-enrichment

✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

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About

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.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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