statgenQTLxT is an R package for fast multi-trait and multi-trial Genome Wide Association Studies (GWAS).
statgenQTLxT has extensive options for summarizing and visualizing results. It builds on the statgenGWAS package (for single trait GWAS) which is available from CRAN. The package uses data structures and plots defined in the statgenGWAS package. It is recommended to read the vignette of this package, accessible in R via vignette(package = "statgenGWAS") or online at https://biometris.github.io/statgenGWAS/articles/GWAS.html to get a general idea of those.
For a full description of the theoretical background and a fully worked example see the vignette.