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GRGL documentation

  • Overview
  • How-to
  • Tutorials
  • Reference
  • Wei Lab
  • GitHub
  • PyPI
  • Overview
  • How-to
  • Tutorials
  • Reference
  • Wei Lab
  • GitHub
  • PyPI

Section Navigation

  • GWAS Tutorial
  • GWAS Tutorial: with covariates
  • PCA Tutorial
  • LinearOperators Tutorial
  • Working with Real Data
  • Working with Simulated Data
  • Simulating Phenotypes
  • Create IGDs and Converting IGD to GRG
  • Converting .vcf.gz to GRG
  • Tutorials

Tutorials#

These tutorials show how to use pygrgl, grapp, and grg_pheno_sim to perform data analysis, filtering, GWAS, and other operations. The tutorials are based on Jupyter notebooks that can be downloaded from here, if you want to run them locally.

  • GWAS Tutorial
    • Get Dataset
    • GWAS via command line
    • GWAS via Python APIs
  • GWAS Tutorial: with covariates
    • Simulate Phenotype
    • Get the top 2 principal components
    • Perform association with covariates
    • Related Topics
  • PCA Tutorial
    • Simulate Data
    • Performing PCA
    • Related Topics
  • LinearOperators Tutorial
    • Get Dataset
    • Related Topics
  • Working with Real Data
    • Build the GRG
    • Examine GRG and allele frequencies
    • Filter the GRG
    • Filter by sample
    • Filter by Mutation
    • Related Topics
  • Working with Simulated Data
    • Simulate Data
    • Convert to GRG
    • Converting to IGD
    • Related Topics
  • Simulating Phenotypes
    • COMING SOON
  • Create IGDs and Converting IGD to GRG
    • Get Dataset
  • Converting .vcf.gz to GRG
    • Get Dataset

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Examples and applications using GRG

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GWAS Tutorial

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