plink2-gwas-analysis
CommunityAnalyze genetic data for disease associations.
Authorjaechang-hits
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates the complex process of performing Genome-Wide Association Studies (GWAS) and population genetics analyses, enabling researchers to identify genetic variants associated with traits or diseases.
Core Features & Use Cases
- Data Conversion: Converts VCF/BGEN files to PLINK binary format for efficient processing.
- Quality Control: Performs rigorous sample and variant QC, including missingness, HWE, and MAF filtering.
- Association Testing: Runs linear or logistic regression GWAS to identify significant genetic associations.
- Population Stratification: Computes Principal Components (PCs) to account for population structure.
- Visualization: Generates Manhattan and QQ plots for visualizing GWAS results.
- Use Case: Analyze a cohort of 10,000 individuals to find genetic markers associated with a specific disease, controlling for population structure.
Quick Start
Run a linear regression GWAS on your PLINK binary files, using phenotypes and covariates, and output the results to a file named 'gwas_result'.
Dependency Matrix
Required Modules
pandasnumpymatplotlibscipy
Components
scriptsreferences
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: plink2-gwas-analysis Download link: https://github.com/jaechang-hits/SciAgent-Skills/archive/main.zip#plink2-gwas-analysis Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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