# Bioresearch Differential Expression

> Perform differential expression (DEG) analysis via the BioResearch Agent biomarker workflow, which computes DEGs (t-test + Bonferroni correction) as its first stage. Use when the user specifically asks for differential expression, DEGs, fold-change, or a volcano plot for a disease or gene-expression dataset.

- **Type:** Skill
- **Install:** `agentstack add skill-alim430-bioresearch-agent-differential-expression`
- **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/differential-expression

## Install

```sh
agentstack add skill-alim430-bioresearch-agent-differential-expression
```

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

## About

# BioResearch Agent — Differential Expression Skill

## Capability

Runs differential expression analysis. In the framework this is the first stage of the
`biomarker` workflow: it loads a gene-expression dataset (GEO or synthetic), performs a t-test
with Bonferroni multiple-testing correction, and emits a DEG table and volcano plot.

## Run

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

(Invokes the biomarker workflow; differential expression is produced in stage 1.)

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

- `biomarker_deg_table.csv` — genes with p-value, adjusted p-value, log2 fold-change
- `biomarker_volcano_plot.png` — volcano plot of DEGs

## Note

There is no standalone `differential-expression` CLI command — DEG is computed inside the
`biomarker` workflow. This skill is a focused entry point that triggers that workflow when the
user's intent is specifically differential expression. 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-differential-expression
- 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%.