Differential expression

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

Install

npx -y skills add Alim430/bioresearch-agent --skill differential-expression

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SKILL.md

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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

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.

What ships with it

Read from the repository

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