bio-causal-genomics-colocalization-analysis SKILL.md skillA
bio-causal-genomics-colocalization-analysis from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-causal-genomics-colocalization-analysis@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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skills/bioskills/bio-causal-genomics-colocalization-analysis/SKILL.md- Versions recorded
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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@sha256:c3cfaae31c1bab8cThe line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
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The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
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