bioresearch-differential-expressionlisted

# 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**.