@article{broman_rqtl2_2019,
	title = {R/qtl2: {Software} for {Mapping} {Quantitative} {Trait} {Loci} with {High}-{Dimensional} {Data} and {Multiparent} {Populations}},
	volume = {211},
	issn = {1943-2631},
	shorttitle = {R/qtl2},
	url = {https://doi.org/10.1534/genetics.118.301595},
	doi = {10.1534/genetics.118.301595},
	abstract = {R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely-used R/qtl software package to include multiparental populations, better handles modern high-dimensional data....R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely used R/qtl software package to include multiparent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes, including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2, which is free and open source software written in the R and C++ programming languages, comes with a test framework.},
	number = {2},
	urldate = {2021-08-18},
	journal = {Genetics},
	author = {Broman, Karl W and Gatti, Daniel M and Simecek, Petr and Furlotte, Nicholas A and Prins, Pjotr and Sen, Śaunak and Yandell, Brian S and Churchill, Gary A},
	month = feb,
	year = {2019},
	pages = {495--502},
}

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The R/qtl2 software expands the scope of the widely-used R/qtl software package to include multiparental populations, better handles modern high-dimensional data....R/qtl2 is an interactive software environment for mapping quantitative trait loci (QTL) in experimental populations. The R/qtl2 software expands the scope of the widely used R/qtl software package to include multiparent populations derived from more than two founder strains, such as the Collaborative Cross and Diversity Outbred mice, heterogeneous stocks, and MAGIC plant populations. R/qtl2 is designed to handle modern high-density genotyping data and high-dimensional molecular phenotypes, including gene expression and proteomics. R/qtl2 includes the ability to perform genome scans using a linear mixed model to account for population structure, and also includes features to impute SNPs based on founder strain genomes and to carry out association mapping. The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. 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The R/qtl2 software provides all of the basic features needed for QTL mapping, including graphical displays and summary reports, and it can be extended through the creation of add-on packages. R/qtl2, which is free and open source software written in the R and C++ programming languages, comes with a test framework.},\n\tnumber = {2},\n\turldate = {2021-08-18},\n\tjournal = {Genetics},\n\tauthor = {Broman, Karl W and Gatti, Daniel M and Simecek, Petr and Furlotte, Nicholas A and Prins, Pjotr and Sen, Śaunak and Yandell, Brian S and Churchill, Gary A},\n\tmonth = feb,\n\tyear = {2019},\n\tpages = {495--502},\n}\n\n","author_short":["Broman, K. W","Gatti, D. M","Simecek, P.","Furlotte, N. A","Prins, P.","Sen, Ś.","Yandell, B. S","Churchill, G. 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