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 packages, qtl2convert (for converting data among the R/qtl2, DOQTL, and R/qtl formats), qtl2fst (for storing genotype probabilities on disk), and qtl2ggplot (for ggplot2-based data visualizations).
Install R/qtl2 from CRAN:
install.packages("qtl2")
- user guide
- categorized list of functions in R/qtl2
- input file formats (also see the sample data files and the qtl2data repository)
- using qtl2fst for on-disk genotype probabilities
- preparing diversity outbred mouse data for R/qtl2
- resources for mouse genome build GRCm39
- genotype diagnostics for diversity outbred mice
- identifying sample mix-ups in diversity outbred mice
- differences between R/qtl and R/qtl2
- developer guide
- HMM benchmarks
- Tutorial on R/qtl2 by Susan McClatchy and Dan Gatti
To cite R/qtl2 in publications, use:
Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen Ś, Yandell BS, Churchill GA (2019) 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
Licensed under GPL-3.