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Bioresearch Differential Expression

skill-alim430-bioresearch-agent-differential-expression · by Alim430

Perform differential expression (DEG) analysis via the BioResearch Agent biomarker workflow, which computes DEGs (t-test + Bonferroni correction) as its first stage. Use when the user specifically asks for differential expression, DEGs, fold-change, or a volcano plot for a disease or gene-expression dataset.

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Install

$ agentstack add skill-alim430-bioresearch-agent-differential-expression

✓ 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 — 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-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.

Source & license

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

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

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Versions

  • v0.1.0 Imported from the upstream source.

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