bio-causal-genomics-mediation-analysis SKILL.md skillA
bio-causal-genomics-mediation-analysis 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-mediation-analysis@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-causal-genomics-mediation-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
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- 34,579 bytes
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- 662
- License
- MIT
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.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file 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@sha256:40bbd1e8b3fe4761The 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_hh63fvnqjosqfs23)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: Frontmatter declares a name
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- pass: Size between 200 bytes and 200 KB (34579 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · 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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