Differential expression

Skill Alim430/bioresearch-agent/skills/biomedical/differential-expression

Executable biomedical workflows for AI assistants — literature analysis, biomarker discovery, and Mendelian randomization through reproducible agent skills.

Install

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

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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.

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.