bio-causal-genomics-mediation-analysis SKILL.md skillA
bio-causal-genomics-mediation-analysis from fridrichmethod/awesome-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add fridrichmethod/awesome-skills/bio-causal-genomics-mediation-analysis@git:20260517.81511a7Pins git:20260517.81511a7 in mdr.lock. Pin the fingerprint instead.
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- SKILL.md skill
- Repository
- fridrichmethod/awesome-skills
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skills/bio-causal-genomics-mediation-analysis/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260517.81511a7, committed May 17, 2026
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- 15
- License
- a license file GitHub does not identify
Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular phenotype mediates the genotype-to-phenotype relationship.
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 stats (base), ggplot2 3.5+
Before using code patterns, verify installed versions match. If versions differ:
- R: `packageVersion('<pkg>')` then `?function_name` to verify parameters
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
# Mediation Analysis
**"Test whether gene expression mediates the effect of this variant on disease"** → Decompose the total genetic effect into direct and indirect (mediated) paths through a molecular phenotype, estimating ACME, ADE, and proportion mediated with bootstrap confidence intervals.
- R: `mediation::mediate()` for causal mediation analysis
## Framework
Causal mediation decomposes the total effect of a treatment (genotype) on an outcome
(phenotype) into:
- **ACME** (Average Causal Mediation Effect) - Indirect effect through the mediator
- **ADE** (Average Direct Effect) - Direct effect not through the mediator
- **Total effect** = ACME + ADE
- **Proportion mediated** = ACME / Total effect
Typical genomic applications:
- SNP -> gene expression (mediator) -> disease
…Read the whole file at its exact version.
How to install
mdr add fridrichmethod/awesome-skills/bio-causal-genomics-mediation-analysis@sha256:40a9193c23f84aa9The line at the top of this page pins the label git:20260517.81511a7, 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_ekp4xryqoluxa4pl)
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Versions
The registry has recorded 1 version of this file, committed on May 17, 2026.
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Source
fridrichmethod/awesome-skills · 15 stars · license a license file GitHub does not identify · pushed 2026-11-02 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ekp4xryqoluxa4pl GET https://markdownregistry.com/api/v1/resolve?ref=fridrichmethod/awesome-skills/bio-causal-genomics-mediation-analysis GET https://markdownregistry.com/api/v1/blob/40a9193c23f84aa96a4ab8d65bfd16528a5fbaf523c8001ea610b8920b1f6ee5
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