# 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.

- **Type:** Skill
- **Install:** `agentstack add skill-alim430-bioresearch-agent-pathway-enrichment`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [Alim430](https://agentstack.voostack.com/s/alim430)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [Alim430](https://github.com/Alim430)
- **Source:** https://github.com/Alim430/bioresearch-agent/tree/main/skills/biomedical/pathway-enrichment

## Install

```sh
agentstack add skill-alim430-bioresearch-agent-pathway-enrichment
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## 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

```bash
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](https://github.com/Alim430)
- **Source:** [Alim430/bioresearch-agent](https://github.com/Alim430/bioresearch-agent)
- **License:** MIT

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

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-alim430-bioresearch-agent-pathway-enrichment
- Seller: https://agentstack.voostack.com/s/alim430
- Browse the marketplace: https://agentstack.voostack.com/browse

---
Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.