# Bioresearch Biomarker Discovery

> Run reproducible biomarker discovery via the BioResearch Agent biomarker workflow (differential expression, pathway enrichment, candidate ranking, volcano plot) over a GEO dataset or synthetic data. Use when the user asks to find gene biomarkers or candidate genes for a disease.

- **Type:** Skill
- **Install:** `agentstack add skill-alim430-bioresearch-agent-biomarker-discovery`
- **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/biomarker-discovery

## Install

```sh
agentstack add skill-alim430-bioresearch-agent-biomarker-discovery
```

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

## About

# BioResearch Agent — Biomarker Discovery Skill

## Capability

End-to-end biomarker discovery: dataset loading (GEO GSE7621 or synthetic) → differential
expression (t-test + Bonferroni) → hypergeometric pathway enrichment (KEGG/GO) → candidate
ranking → volcano plot. Returns ranked candidate biomarkers, not just a narrative.

## Run

```bash
bioresearch run biomarker --disease "Parkinson's disease"
```

## Outputs (in `outputs/biomarker/`)

- `biomarker_deg_table.csv` — differentially expressed genes
- `biomarker_top_candidates.csv` — ranked candidates
- `biomarker_pathway_enrichment.csv` — enriched pathways / GO terms
- `biomarker_volcano_plot.png` — volcano plot
- `biomarker_report.txt` — structured report

## Note

This skill dispatches to the framework's `biomarker` workflow. It adds **no analysis of its
own**; all statistics run in the workflow modules. Requires no LLM key.

## 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-biomarker-discovery
- Seller: https://agentstack.voostack.com/s/alim430
- Browse the marketplace: https://agentstack.voostack.com/browse

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