bio-causal-genomics-colocalization-analysis skillA
bio-causal-genomics-colocalization-analysis is agent-read markdown (skill) from pku-yuangroup/openai4s: Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization..
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What the file says
## Version Compatibility
Reference examples tested with: coloc 5.2.3+, susieR 0.12.35+, hyprcoloc 1.0+ (GitHub jrs95/hyprcoloc), SMR 1.3.1+ (CLI, cnsgenomics.com), eCAVIAR 2.2+ (compiled from caviar/eCAVIAR repo), PWCoCo 1.0+ (jwr-git/pwcoco), moloc 0.1+ (clagiamba/moloc), SharePro_coloc 7.0+ (zhwm/SharePro_coloc), R >= 4.1.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('coloc')`; check `?coloc.abf`, `?coloc.susie`, `?runsusie`
- CLI: `smr --version`, `pwcoco --help`, `sharepro_coloc.py --help`
If code throws AttributeError, NULL list elements, or `Error in coloc.abf: dataset must have...`, introspect the installed package signature and adapt the example rather than retrying.
# Colocalization Analysis
**"Test whether my GWAS signal and an eQTL share the same causal variant"** -> Compute Bayesian posterior probabilities over five hypotheses (H0 neither, H1 trait-1-only, H2 trait-2-only, H3 distinct causal variants, H4 shared causal variant) to discriminate true causal overlap from LD-driven coincidence, then run sensitivity analysis over the p12 prior.
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How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-colocalization-analysis@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-causal-genomics-colocalization-analysis@sha256:c3cfaae31c1bab8cPin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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