bio-causal-genomics-genomic-sem skillA
bio-causal-genomics-genomic-sem is agent-read markdown (skill) from pku-yuangroup/openai4s: Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling l.
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What the file says
## Version Compatibility
Reference examples tested with: GenomicSEM 0.0.5+ (GitHub `GenomicSEM/GenomicSEM`), lavaan 0.6-17+, LDSC v1.0.1+ (Python 3; prefer `abdenlab/ldsc-python3` v2.0.0 -- `belowlab/ldsc` v3.0.1 README states the CLI is broken; Docker `jtb114/ldsc:latest` is the belowlab fallback), baselineLD_v2.2 annotations (alkesgroup.broadinstitute.org/LDSCORE), MTAG 1.0.8+ (Python; `JonJala/mtag`), R 4.4+.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('GenomicSEM')` then `?ldsc`, `?commonfactor`, `?usermodel`, `?commonfactorGWAS`
- Python (LDSC, MTAG): `<tool>.py -h` and inspect the source under `ldsc/` or `mtag/`
GenomicSEM is GitHub-only (never on CRAN). If `ldsc()` or `usermodel()` throws an error about lavaan syntax or non-positive-definite covariance, introspect the installed API (`getMethod('ldsc')`) and adapt rather than retrying.
# Genomic SEM
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How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-genomic-sem@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-causal-genomics-genomic-sem@sha256:05bad8d5580e00edPin 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_emivionuhv5io2cm)
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Audit of the latest version
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Source
pku-yuangroup/openai4s · 586 stars · license MIT · pushed 2026-09-23 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_emivionuhv5io2cm GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-causal-genomics-genomic-sem GET https://markdownregistry.com/api/v1/blob/05bad8d5580e00ed704206855343c74a146ef74430033b96c1ab021458b628b5
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