Bioresearch Biomarker Discovery

Run reproducible biomarker discovery via the BioResearch Agent biomarker workflow (differential expression, pathway enrichment, candidate ranking, volcano plot) over a GEO dataset or synthetic data. Use when the user asks to find gene biomarkers or candidate genes for a disease.

Alim430 Updated

File contents

BioResearch Agent — Biomarker Discovery Skill

Capability

End-to-end biomarker discovery: dataset loading (GEO GSE7621 or synthetic) → differential expression (t-test + Bonferroni) → hypergeometric pathway enrichment (KEGG/GO) → candidate ranking → volcano plot. Returns ranked candidate biomarkers, not just a narrative.

Run

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

Outputs (in outputs/biomarker/)

  • biomarker_deg_table.csv — differentially expressed genes
  • biomarker_top_candidates.csv — ranked candidates
  • biomarker_pathway_enrichment.csv — enriched pathways / GO terms
  • biomarker_volcano_plot.png — volcano plot
  • biomarker_report.txt — structured report

Note

This skill dispatches to the framework's biomarker workflow. It adds no analysis of its own; all statistics run in the workflow modules. Requires no LLM key.

Alim430/bioresearch-agent/tree/main/skills/biomedical/biomarker-discovery commit a732d6585e

Frequently asked questions

npx skillmds@latest add alim430/bioresearch-biomarker-discovery