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

Discussion group

For discussion/questions about R/qtl2, join the rqtl2-disc google group. Or join rqtl-announce for announcements about R/qtl and R/qtl2. (We’ll try to keep the original rqtl-disc group for the discussion/questions about the original R/qtl only.)


R/qtl2 is not yet available on CRAN, but it can be installed from a mini-CRAN at rqtl.org. Make sure you have the latest version of R.

install.packages("qtl2", repos="http://rqtl.org/qtl2cran")

Alternatively, you can install R/qtl2 from its source on GitHub. (But note that compiling the C++ code can be rather slow.)

On Windows, you’ll need Rtools.

On Mac OS X, you’ll need the command-line developer tools.

You then need to install the devtools package, plus a set of package dependencies: yaml, jsonlite, data.table, RcppEigen, RSQLite, and qtl. (Additional, secondary dependencies will also be installed.)

install.packages(c("devtools", "yaml", "jsonlite", "data.table", "RcppEigen", "RSQLite", "qtl"))

Finally, install R/qtl2 using devtools::install_github().




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. bioRxiv doi:10.1101/414748


Licensed under GPL-3.

Sources on github: