bio-causal-genomics-effector-gene-prioritization skillA
bio-causal-genomics-effector-gene-prioritization is agent-read markdown (skill) from pku-yuangroup/openai4s: Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 2023), FLAMES, INQUISIT, DEPICT, and enhancer-gene predictors (ABC, ENCODE-rE2G). Use when narrowing a GWAS lead locus to a candidate causal gene, picking between proximity, eQTL-based, and similarity-based.
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: MAGMA 1.10+ (cncr.nl/research/magma), FUMA web platform v1.6+ (fuma.ctglab.nl), Open Targets Genetics API (REST + GraphQL, June 2024 release), PoPS (head of `FinucaneLab/pops`, 2024), cS2G pre-computed scores (Zenodo record 7754032, Gazal 2022), ABC-Enhancer-Gene-Prediction 0.2.2+, ENCODE-rE2G v1.0+ (Gschwind 2023 preprint), DEPICT v1 rel194, INQUISIT (Fachal 2020 supplementary), Python 3.9-3.11, R 4.3+, PLINK 1.9 + PLINK 2.0.
Before using code patterns, verify installed versions match. If versions differ:
- CLI: `magma --help` to confirm gene-window, gene-annot, and gene-set flag names
- Python: `pip show gentropy`; introspect endpoints at `api.platform.opentargets.org/api/v4/graphql`
- R: `packageVersion('coloc')` etc. for upstream evidence integration
If a script throws an error about an argument that has moved (e.g. an Open Targets endpoint renamed during a release) or a model file schema change, introspect the installed tool and adapt rather than retrying. Open Targets Genetics deprecated the standalone Genetics Portal in 2024 in favour of the integrated platform; verify endpoint URLs at the time of use.
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-effector-gene-prioritization@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-causal-genomics-effector-gene-prioritization@sha256:6f3d1f3833aff4f2Pin 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_etl4mxi7ze2ym74n)
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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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