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JWAS.jl

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JWAS

JWAS.jl is an open-source software tool written in Julia for Bayesian multiple regression methods applied to genomic prediction and genome-wide association studies.

Structure of JWAS

  flowchart TD;
      A["phenotypes.csv"] --> A2(CSV.read) --> D(build_model)
      B["pedigree.csv"] --> B2(get_pedigree) --> D(build_model)
      C["genotypes.csv"] --> C2(get_genotypes) --> D(build_model)
      D --> E(set_covariate);
      D --> F(set_random);
      E --> H{runMCMC}
      F --> H

Help

  1. Show this README file in REPL or notebook using ?JWAS
  2. For help on a specific function above, type ? followed by its name, e.g. ?runMCMC and press enter.
  3. Run Pkg.add(PackageSpec(name="JWAS", rev="master")) to get the newest unofficial JWAS. Run Pkg.free("JWAS") to go back to the official one.

Examples available here

  • Single Trait Analysis
  • Multiple Trait Analysis
  • Repeated Measures
  • Single Step Analysis
  • Categorical Trait Analysis
  • Censored Trait Analysis
  • Joint Analysis of Continuous, Categorical, and Censored Traits
  • Multi-class Bayesian Analysis
  • Neural Networks (NN-MM)
  • Cross Validation
  • Genome Wide Association Study
  • Integrating Phenotypic Causal Networks in GWAS
  • single trait and multiple trait GBLUP by providing the relationship matrix directly
  • Description of Mixed Effects Model
  • Quality Control of Genotypes