Alim430 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-changebiomarker_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.