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Bioresearch Causal Evidence

skill-alim430-bioresearch-agent-causal-evidence · by Alim430

Run the causal-evidence chain (GWAS → eQTL → colocalization → TWAS → fine-mapping → MR) via the BioResearch Agent causal-evidence workflow. Use when the user wants to test whether a GWAS risk locus acts through a candidate gene's expression, identify the credible set, and check MR consistency. Synthetic loci by default; methodology validation, not a real etiological claim.

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Install

$ agentstack add skill-alim430-bioresearch-agent-causal-evidence

✓ 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 — Causal Evidence Chain Skill

Capability

Runs the full causal-evidence chain for a set of loci:

  1. GWAS → eQTL — per-SNP association in both trait and expression.
  2. Colocalization — full 5-hypothesis coloc (Giambartolomei 2014), reporting PP.H4

(shared causal variant) vs PP.H3 (distinct variants). Numerically stable (log-space ABF).

  1. TWAS — S-PrediXcan-style expression-trait association (Z, p).
  2. Fine-mapping — Bayesian credible set via per-SNP posterior inclusion probability (PIP),

normalized over the locus.

  1. MR — Wald-ratio causal estimate for the colocalized gene's lead SNP.

Returns a per-gene evidence table + credible-set CSV + locus heatmap, not a biological claim.

Run

bioresearch run causal-evidence --seed 42 --output-dir outputs/causal-evidence

Outputs (in --output-dir)

  • CE_per_gene_results.csv — per-gene: truth class, PP.H4, TWAS Z/p, MR β/p, n credible
  • CE_credible_sets.csv — per-SNP PIP + credible-set membership
  • CE_locus_heatmap.png — GWAS / eQTL / coloc association heatmap
  • CE_recovery_benchmark.csv — ground-truth recovery across effect sizes
  • CE_summary_report.txt — human-readable summary
  • CE_evidence_package.json — reproducible Evidence Package (provenance + benchmark + grade)

Note

This skill dispatches to the framework's causal-evidence workflow / demo_causal_evidence.py. It adds no analysis of its own; all statistics run in the workflow modules. By default uses synthetic loci with ground-truth labels to validate the engine — real-data AD reference loci (TREM2 / BIN1 / APOE / CLU / PICALM) are listed as the target for a real-data version. Evidence grade is C (methodology validation).

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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