bio-causal-genomics-genetic-correlation skillA
bio-causal-genomics-genetic-correlation is agent-read markdown (skill) from pku-yuangroup/openai4s: Estimates bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity.
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.
What the file says
## Version Compatibility
Reference examples tested with: LDSC v1.0.1+ (Python 3; prefer `abdenlab/ldsc-python3` v2.0.0 -- `belowlab/ldsc` v3.0.1 README states the `--h2 / --rg / --h2-cts` CLI is broken; use Docker `jtb114/ldsc:latest` for the belowlab fallback; original `bulik/ldsc` is Python 2.7 unmaintained since 2019), HDL 1.4.0+ (R; GitHub `zhenin/HDL`), LAVA 0.1.0+ (R; GitHub `josefin-werme/LAVA`), HESS 0.5.4+ (Python; huwenboshi/hess), Popcorn 1.0+ (Python; brielin/Popcorn), GCTA 1.94+ (GREML-bivariate), baselineLD_v2.2 / eur_w_ld_chr LD-score panels from alkesgroup.broadinstitute.org/LDSCORE, UKB-array SVD eigen reference for HDL.
Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `python3 -c 'import <module>; help(<module>)'`
- R: `packageVersion('<pkg>')` then `?function_name`
- CLI: `<tool> --version` then `<tool> --help`
If code throws an LD-score "category not found" error, an HDL reference-panel mismatch, or a LAVA locus-ID lookup failure, introspect the installed LD-score column headers and the supplied partitioning file rather than retrying with default flags.
# Genetic Correlation
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How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-genetic-correlation@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-causal-genomics-genetic-correlation@sha256:a52d58a7422a40d9Pin 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.
[](https://markdownregistry.com/a/art_vgfl5xwqabrinz47)
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Versions
Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
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