bio-causal-genomics-heritability-partitioning SKILL.md skillA
bio-causal-genomics-heritability-partitioning 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-heritability-partitioning@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
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- pku-yuangroup/openai4s
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skills/bioskills/bio-causal-genomics-heritability-partitioning/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- License
- MIT
Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories…
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What the file says
## Version Compatibility
Reference examples tested with: LDSC v1.0.1+ (Python 3 fork; prefer `abdenlab/ldsc-python3` v2.0.0 which retains the working `--h2 / --rg / --h2-cts` CLI -- `belowlab/ldsc` v3.0.1 explicitly broke that CLI per its README and is best run via Docker `jtb114/ldsc:latest`), LDAK 6.0+, BOLT-LMM 2.4.1+, GCTA 1.94+, HESS 0.5.4+, HDL 1.4.0+ (R; GitHub `zhenin/HDL`), Popcorn 1.0+ (Python; brielin/Popcorn), baselineLD_v2.2 annotations (alkesgroup.broadinstitute.org/LDSCORE).
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`
LDSC's official repository (bulik/ldsc) is Python 2.7 only and unmaintained since 2019; use the Python 3 community forks. If code throws ImportError, AttributeError, or a "category not found" error in the LD score file, introspect the installed binary and the actual LD-score column headers rather than retrying.
# Heritability Partitioning
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How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-heritability-partitioning@sha256:ec495372e522fdfeThe 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.
[](https://markdownregistry.com/a/art_yzizlynbywy4crhe)
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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
GET https://markdownregistry.com/api/v1/artifacts/art_yzizlynbywy4crhe GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-causal-genomics-heritability-partitioning GET https://markdownregistry.com/api/v1/blob/ec495372e522fdfead9faef79f3dc492ca6c555798206039bef26aec0e591d06
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