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Bioresearch Biomarker Discovery

Name: Bioresearch Biomarker Discovery
Availability: InStock
Author: Alim430

skill-alim430-bioresearch-agent-biomarker-discovery · by Alim430

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.

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Install

$ agentstack add skill-alim430-bioresearch-agent-biomarker-discovery

✓ scanned · ✓ verified — works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

✓ Prompt-injection patterns
✓ Secret / credential exfiltration
✓ Dangerous shell & filesystem operations
✓ Untrusted network calls
✓ Known-malicious package signatures

What it can access

✓ Network access No
✓ Filesystem access No
✓ Shell / process execution No
✓ Environment & secrets No
✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

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About

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.

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Author: Alim430
Source: Alim430/bioresearch-agent
License: MIT

Install and usage instructions live in the source repository linked above.

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Versions

v0.1.0 Imported from the upstream source.