QTL analysis software for high-dimensional data and complex cross designs
Branch: master
Clone or download
kbroman Make tests that download only run locally
- tests of index_snps() and genoprob_to_snpprobs()
Latest commit b5785d5 Feb 16, 2019
Type Name Latest commit message Commit time
Failed to load latest commit information.
R zip_datafiles(): return value didn't include the directory Feb 16, 2019
data Small change to original CC colors Feb 17, 2018
inst Add accent to Saunak in citation Feb 8, 2019
man Add function calc_het(); implements Issue #64 Jan 23, 2019
src Fix a bug in the step probabilities for the new genail cross type Feb 2, 2019
.Rbuildignore Rename ReadMe.md and License.md in all caps Feb 27, 2018
.travis.yml .travis.yml: shorter dir path for install log Jan 31, 2019
DESCRIPTION Increase tolerance in a few tests Feb 16, 2019
Makefile Makefile: add "make test" [skip ci] Nov 8, 2017
NEWS.md Increase tolerance in a few tests Feb 16, 2019



Build Status

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.

It was previously split into the multiple packages qtl2geno, qtl2scan, qtl2plot, and qtl2db, but that proved awkward and confusing and so the packages have been combined. But also see the related package, qtl2convert, for converting data among the R/qtl2, DOQTL, and R/qtl formats. qtl2convert will remain a separate package.


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. Genetics 211:495-502 doi:10.1534/genetics.118.301595


Licensed under GPL-3.