Flexible Multivariate Linear Mixed Model based QTL Analysis for Structured Multiple Traits
FlxQTL.jl is a package for a multivariate linear mixed model based QTL analysis tool that supports incorporating information from trait covariates such as time or different environments. The package supports computation of one-dimensional and two-dimensional multivariate genome scans, visualization of genome scans, support for LOCO (leave-one-chromosome-out), computation of kinship matrices, and support for distributed computing.
The package is written in Julia and includes extensive documentation. If you are new to Julia you may want to learn more by looking at Julia documentation. Example data sets are located in the data directory. For details about the method, you may want to read our paper available as a preprint.
Flexible multivariate linear mixed models for structured multiple
Hyeonju Kim, Gregory Farage, John T. Lovell, John K. Mckay, Thomas E. Juenger, Śaunak Sen
The package can installed in following ways.
In a Julia REPL, press
] to enter a package mode,
julia> ] pkg> add FlxQTL
julia> using Pkg; Pkg.add("FlxQTL")
For installing from the source,
pkg> add https://github.com/senresearch/FlxQTL.jl
1.5 supports for the package.
To remove the package from the Julia REPL,
julia> ] pkg> rm FlxQTL
julia> using Pkg; Pkg.rm("FlxQTL")
Choice of BLAS vendors
The package can be run with OpenBLAS (built-in Julia dense linear
algebra routines) or MKL (Intel's Math Kernel Library).
works best on Intel hardware, but it can slightly improve performance
without Intel hardware. For installation and details,