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

JWAS.jl

├────── get_pedigree
├────── get_genotypes
├────── build_model
├────── set_covariate
├────── set_random
├────── solve
├────── runMCMC
└────── ...

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
• Multi-class Bayesian Analysis
• Neural Networks
• 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