AR
数据与复现
arxiv-database
arxiv-database：This skill provides Python tools ，用于 searching 、 retrieving preprints ，面向 arXiv.org ，通过 its public Atom A…
K-Dense-AI/claude-scientific-skills查看
数据与复现
BI
bio-causal-genomics-mediation-analysis
维护者 FreedomIntelligence · 最近更新 2026年4月1日
bio-causal-genomics-mediation-analysis：Decompose genetic effects into direct 、 indirect paths through mediating variables ，使用 mediation R package。 Tests whether gene expression，methylation，或 other molecular phenotypes mediate effect of genetic variants on disease。 适合在testing whether molecular phenotype mediates genotype-to-phenotype relationship时使用。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-causal-genomics-mediation-analysis
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- R：mediation：：mediate() ，用于 causal mediation analysis。
- Test whether gene expression mediates effect of this variant on disease" → Decompose total genetic effect into direct 、 indirect (mediated) paths through molecular phenotype，estimating ACME，ADE，、 proportion mediated ，支持 bootstrap confidence intervals. R：mediation：：mediate() ，用于 causal mediation analysis。
- mediator_model <- lm(expression ~ genotype + age + sex + pc1 + pc2，data = dat)。
原始文档
SKILL.md 摘录
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
- SNP -> DNA methylation (mediator) -> gene expression
- SNP -> protein levels (mediator) -> clinical outcome
Basic Mediation with the mediation Package
Goal: Decompose a genetic effect into direct and indirect (mediated) paths through a molecular phenotype.
Approach: Fit separate models for mediator and outcome, then run mediate() with bootstrap to estimate ACME (indirect), ADE (direct), and proportion mediated.
library(mediation)
## For binary outcome, use glm with family = binomial
outcome_model <- glm(
disease ~ genotype + expression + age + sex + pc1 + pc2,
data = dat, family = binomial
)
适用场景
- 适合在testing whether molecular phenotype mediates genotype-to-phenotype relationship时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- mendelian-randomization - Causal inference using genetic instruments
- colocalization-analysis - Test if signals share a causal variant
- population-genetics/association-testing - GWAS for treatment-outcome associations
- multi-omics-integration/mofa-integration - Multi-omics data for mediation chains
相关技能
相关技能
BA
数据与复现
bayesian-optimizer
bayesian-optimizer：Bayesian optimization ，用于 experimental design 、 hyperparameter tuning in biomedical research。
FreedomIntelligence/OpenClaw-Medical-Skills查看
bio-alignment-files-bam-statistics：Compute alignment statistics：flagstat，idxstats，coverage depth。
FreedomIntelligence/OpenClaw-Medical-Skills查看
BI
bio-alignment-msa-statistics：Calculate alignment statistics ，涵盖 sequence identity，conservation scores，substitution matri…
FreedomIntelligence/OpenClaw-Medical-Skills查看