R/qtl2

Karl Broman

R/qtl2 (aka qtl2) is a reimplementation of the QTL analysis software R/qtl, to better handle high-dimensional data and complex cross designs.

Also see the related package, qtl2convert, for converting data among the R/qtl2, DOQTL, and R/qtl formats.

Installation

Install R/qtl2 from CRAN:

install.packages("qtl2")

Vignettes

• user guide
• input file formats (see also the sample data files and the qtl2data repository)
• preparing DO mouse data for R/qtl2
• differences between R/qtl and R/qtl2
• developer guide
• HMM benchmarks

Citation

To cite R/qtl2 in publications, use:

Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2018) R/qtl2: software for mapping quantitative trait loci with high-dimensional data and multi-parent populations. Genetics 211:495-502 doi:10.1534/genetics.118.301595

License

Licensed under GPL-3.