Causal inference

Skill Alim430/bioresearch-agent/skills/biomedical/causal-inference

Run two-sample Mendelian randomization via the BioResearch Agent causal workflow (IVW estimation, leave-one-out sensitivity, scatter / funnel plots). Use when the user asks to test a causal effect between an exposure and an outcome (e.g., BMI → Type 2 Diabetes) using genetic instruments.From its SKILL.md

Install

npx -y skills add Alim430/bioresearch-agent --skill causal-inference

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One thing to look at

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SKILL.md

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BioResearch Agent — Causal Inference (MR) Skill

Capability

Runs a reproducible two-sample Mendelian randomization: GWAS summary statistics (simulated by default) → genome-wide significant SNP instruments → IVW causal estimate → leave-one-out sensitivity → scatter / funnel plots. Returns a quantitative causal estimate, not a claim.

Run

bioresearch run causal --exposure BMI --outcome "Type 2 Diabetes"

Outputs (in `outputs/causal/`)

causal_ivw_results.csv — IVW estimate, SE, p-value
causal_loo_results.csv — leave-one-out sensitivity
causal_mr_scatter.png — MR scatter plot (IVW slope labeled)
causal_mr_funnel.png — funnel plot
causal_interpretation.txt — interpretation notes

Note

This skill dispatches to the framework's causal workflow. It adds no analysis of its own; all MR statistics run in the workflow modules. By default uses simulated GWAS data (no external credentials required).

What ships with it

Read from the repository

Just SKILL.md. No reference files, no scripts.