bio-causal-genomics-mediation-analysis skillA
bio-causal-genomics-mediation-analysis is agent-read markdown (skill) from pku-yuangroup/openai4s: Decompose total effects into direct and indirect paths through mediators using mediation, CMAverse 4-way, HIMA/HIMA2 high-dimensional, BAMA, two-step / MVMR mediation, or double-ML medDML. Use when testing whether a molecular phenotype (expression, methylation, protein) mediates a treatment-outcome relationship, decomposing exposure-mediator interaction via VanderWeele 4-way, screening high-dimensional EWAS mediators, or running MR-based mediation when sequential ignorability is implausible..
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: R 4.3+, mediation 4.5.0+, CMAverse 0.1.0+ (GitHub `BS1125/CMAverse`), HIMA >= 2.3.0 (GitHub `YinanZheng/HIMA`; archived from CRAN 2026-07), bama 1.3+, causalweight 1.0.5+ (medDML), MVMR 0.4+, TwoSampleMR 0.6+, EValue 4.1+, gesttools 1.3+, ipw 1.0.11+.
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
- HIMA must be pinned at `>= 2.3.0` for the code patterns below; the formula interface `hima(formula, data.pheno, data.M, mediator.type, penalty, ...)` was introduced in 2.3.0. On HIMA 2.2.x the classic engine is the top-level `hima(X, Y, M, COV.XM=, COV.MY=, Y.family=, penalty=)` (positional order X, Y, M) with no formula interface; HIMA 2.2.x is NOT API-compatible with the examples here.
- In 2.3+ the classic engine is `hima_classic(X, M, Y, COV.XM=, COV.MY=, Y.type=)` (positional order X, M, Y; outcome type via `Y.type`, not `Y.family`); use it only to reproduce the original 2016-2021 SIS+penalty pipelines.
…Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-causal-genomics-mediation-analysis@git:20260821.2d1b678mdr add pku-yuangroup/openai4s/bio-causal-genomics-mediation-analysis@sha256:40bbd1e8b3fe4761Pin 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_hh63fvnqjosqfs23)
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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
GET https://markdownregistry.com/api/v1/artifacts/art_hh63fvnqjosqfs23 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-causal-genomics-mediation-analysis GET https://markdownregistry.com/api/v1/blob/40bbd1e8b3fe476195dadaf6b6c08313a26abb1fcc8573ddba56c2a5284d141d
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