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JWAS.jl

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.

• Homepage: QTL.rocks
• Discussion group: available here
• Installation: at the Julia REPL, using Pkg; Pkg.add("JWAS")
• Documentation: available here
• Examples: available here
• Authors: Hao Cheng, Rohan Fernando, Dorian Garrick

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