bio-population-genetics-association-testing
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests.
npx skills add BioTender-max/awesome-bio-agent-skills --skill association-testing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scipy 1.12+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Association Testing **"Run a GWAS on my genotyping data"** → Perform genome-wide association testing using logistic (case-control) or linear (quantitative) regression with covariates, then visualize results with Manhattan and QQ plots. - CLI: `plink2 --glm` for association testing with covariates GWAS analysis using PLINK 2.0's unified `--glm` command for case-control and quantitative traits. ## PLINK 2.0 Association Testing ### Basic Case-Control (Binary Phenotype) ```bash # Basic logistic regression plink2 --bfile data --glm --out results # With phenotype file plink2 --bfile data --pheno pheno.txt --glm --out results ``` ### Quantitative Trait (Continuous Phenotype) ```bash # Linear regressi
- Version Compatibility
- PLINK 2.0 Association Testing
- Basic Case-Control (Binary Phenotype)
- Quantitative Trait (Continuous Phenotype)
- With Covariates
- Covariate Files
- Phenotype File Format
- Covariate File Format
- GLM Options
- Phenotype Handling
- Model Options
- Firth Regression (Rare Variants)
- Output Format
- Output Columns
Basic logistic regression plink2 --bfile data --glm --out results With phenotype file plink2 --bfile data --pheno pheno.txt --glm --out results Linear regression for quantitative traits Include covariates (sex, age, PCs) plink2 --bfile data \ Specify which covariates to use Multiple phenotypes (test all) plink2 --bfile data --pheno pheno_multi.txt --glm --out results
What does the bio-population-genetics-association-testing skill do?
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill association-testing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.