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R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations
Open accessAbstract
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.
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R: A Language and Environment for Statistical Computing
R Core Team (2025) · doi:10.32614/r.manuals · Cited by 352,181
A Direct Approach to False Discovery Rates
Storey, J. D. (2002) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/1467-9868.00346 · Cited by 5,603
Mapping mendelian factors underlying quantitative traits using RFLP linkage maps.
Lander, E. S., & Botstein, D. (1989) · Genetics · doi:10.1093/genetics/121.1.185 · Cited by 5,235
Empirical threshold values for quantitative trait mapping.
Churchill, G. A., & Doerge, R. W. (1994) · Genetics · doi:10.1093/genetics/138.3.963 · Cited by 4,935
Self-citationYu, J., Pressoir, G., Briggs, W. H., Vroh Bi, I., Yamasaki, M., Doebley, J. F., McMullen, M. D., Gaut, B. S., Nielsen, D. M., Holland, J. B., et al. (2006) · Nature Genetics · doi:10.1038/ng1702 · Cited by 4,133
R/qtl: QTL mapping in experimental crosses
Broman, K. W., Wu, H., Sen, Ś., & Churchill, G. A. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg112 · Cited by 3,463
Self-citationThe Split-Apply-Combine Strategy for Data Analysis
Wickham, H. (2011) · Journal of Statistical Software · doi:10.18637/jss.v040.i01 · Cited by 2,705
The positive false discovery rate: a Bayesian interpretation and the q-value
Storey, J. D. (2003) · The Annals of Statistics · doi:10.1214/aos/1074290335 · Cited by 2,204
Haley, C. S., & Knott, S. A. (1992) · Heredity · doi:10.1038/hdy.1992.131 · Cited by 1,991
Efficient Control of Population Structure in Model Organism Association Mapping
Kang, H. M., Zaitlen, N. A., Wade, C. M., Kirby, A., Heckerman, D., Daly, M. J., & Eskin, E. (2008) · Genetics · doi:10.1534/genetics.107.080101 · Cited by 1,835
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Metadata
- Authors
- Broman, K. W., Gatti, D. M., Simecek, P., Furlotte, N. A., Prins, P., Sen, Ś., Yandell, B. S., & Churchill, G. A.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-02-01
- Volume
- 211
- Issue
- 2
- Pages
- 495-502
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2950395494
- Cited by
- 452
- References
- 57
- FWCI
- 20.82
- Type
- journal article
- Language
- en
- Open access
- green
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- Broman, K. W., Gatti, D. M., Simecek, P., Furlotte, N. A., Prins, P., Sen, Ś., Yandell, B. S., & Churchill, G. A. (2019). R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations. Genetics. https://doi.org/10.1534/genetics.118.301595
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