### [R/qtl2](https://kbroman.org/qtl2/) <a href="https://kbroman.org/qtl2/"><img src="https://kbroman.org/qtl2/assets/pics/qtl2_logo.png" align="right" height="138" alt="R/qtl2 logo"/></a>

[![R-CMD-check](https://github.com/rqtl/qtl2/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/rqtl/qtl2/actions/workflows/R-CMD-check.yaml)
[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/qtl2)](https://cran.r-project.org/package=qtl2)
[![r-universe badge](https://rqtl.r-universe.dev/qtl2/badges/version)](https://rqtl.r-universe.dev/qtl2)
[![zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3237772.svg)](https://doi.org/10.5281/zenodo.3237772)

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

Also see the related packages,
[qtl2convert](https://github.com/rqtl/qtl2convert) (for converting
data among the R/qtl2, DOQTL, and R/qtl formats),
[qtl2fst](https://github.com/rqtl/qtl2fst) (for storing genotype
probabilities on disk), and [qtl2ggplot](https://github.com/byandell-sysgen/qtl2ggplot)
(for [ggplot2](https://ggplot2.tidyverse.org/)-based data visualizations).

---

### Installation

Install R/qtl2 from [CRAN](https://cran.r-project.org):

```r
install.packages("qtl2")
```

Alternatively, install it from [R
universe](https://rqtl.r-universe.dev):

```r
install.packages("qtl2", repos=c("https://rqtl.r-universe.dev",
                                 "https://cloud.r-project.org"))
```

Or use [remotes](https://remotes.r-lib.org) to install it from its GitHub source:

```r
install.packages("remotes")
remotes::install_github("rqtl/qtl2")
```

---

### Documentation

- [user guide](https://kbroman.org/qtl2/assets/vignettes/user_guide.html)
- [categorized list of functions in R/qtl2](https://kbroman.org/qtl2/pages/rqtl2_functions.html)
- [input file formats](https://kbroman.org/qtl2/assets/vignettes/input_files.html)
  (also see the
  [sample data files](https://kbroman.org/qtl2/pages/sampledata.html)
  and the [qtl2data repository](https://github.com/rqtl/qtl2data))
- [using qtl2fst for on-disk genotype probabilities](https://kbroman.org/qtl2/assets/vignettes/qtl2fst.html)
- [preparing diversity outbred mouse data for R/qtl2](https://kbroman.org/qtl2/pages/prep_do_data.html)
- [resources for mouse genome build GRCm39](https://kbroman.org/qtl2/pages/move_to_build39.html)
- [genotype diagnostics for diversity outbred mice](https://kbroman.org/qtl2/assets/vignettes/do_diagnostics.html)
- [identifying sample mix-ups in diversity outbred mice](https://kbroman.org/qtl2/assets/vignettes/do_mixups.html)
- [differences between R/qtl and R/qtl2](https://kbroman.org/qtl2/assets/vignettes/rqtl_diff.html)
- [developer guide](https://kbroman.org/qtl2/assets/vignettes/developer_guide.html)
- [HMM benchmarks](https://kbroman.org/qtl2/assets/vignettes/hmm_benchmarks.html)
- [Tutorial on R/qtl2](https://smcclatchy.github.io/mapping/) by [Susan McClatchy](https://github.com/smcclatchy) and
  [Dan Gatti](https://github.com/dmgatti)
- [`scan1gen` examples](https://kbroman.org/qtl2/assets/vignettes/scan1gen.html)

---

### Citation

To cite R/qtl2 in publications, use:

> Broman KW, Gatti DM, Simecek P, Furlotte NA, Prins P, Sen &#346;,
> 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](https://doi.org/10.1534/genetics.118.301595)

---

### License

Licensed under [GPL-3](https://www.r-project.org/Licenses/GPL-3).
