Biomarker discovery

Skill Alim430/bioresearch-agent/skills/biomedical/biomarker-discovery

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 biomarker-discovery

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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.

SKILL.md

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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.