R/qtl: high-throughput multiple QTL mapping

Danny Arends; Pjotr Prins; Ritsert C. Jansen; Karl W. Broman

doi:10.1093/bioinformatics/btq565

R/qtl: high-throughput multiple QTL mapping

Danny Arends, Pjotr Prins, Ritsert C. Jansen, Karl W. Broman

Research output: Contribution to journal › Article › peer-review

310 Citations (Scopus)

Abstract

Motivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.Contact:[email protected]

Original language	English
Pages (from-to)	2990-2992
Number of pages	3
Journal	Bioinformatics
Volume	26
Issue number	23
DOIs	https://doi.org/10.1093/bioinformatics/btq565
Publication status	Published - 1 Oct 2010
Externally published	Yes

Access to Document

10.1093/bioinformatics/btq565

https://doi.org/10.1093/bioinformatics/btq565

310 Citations
3 Article
1 Book

High-throughput computational methods and software for quantitative trait locus (QTL) mapping
Arends, D., 2014, 1 ed. Groningen: Danny Arends. 169 p.
Research output: Book/Report › Book › peer-review

Open Access
Integrative genomic approach identifies multiple genes involved in cardiac collagen deposition
Lodder, E. M., Scicluna, B. P., Beekman, L., Arends, D., Moerland, P. D., Tanck, M. W. T., Adriaens, M. E. & Bezzina, C. R., 1 Dec 2014, In: Circulation: Cardiovascular Genetics. 7, 6, p. 790-798 9 p.
Research output: Contribution to journal › Article › peer-review

Open Access
12 Citations (Scopus)
Identifying genotype-by-environment interactions in the metabolism of germinating arabidopsis seeds using generalized genetical genomics
Louis Joosen, R. V., Arends, D., Li, Y., Willems, L. A. J., Keurentjes, J. J. B., Ligterink, W., Jansen, R. C. & Hilhorst, H. W. M., Jun 2013, In: Plant Physiology. 162, 2, p. 553-566 14 p.
Research output: Contribution to journal › Article › peer-review

Open Access
47 Citations (Scopus)

1 Invited talk

Novel Methods in Quantitative Trait Analysis (QTL)
Arends, D. (Speaker)
19 Dec 2022
Activity: Talk or presentation › Invited talk

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Cite this

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title = "R/qtl: high-throughput multiple QTL mapping",

abstract = "Motivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.Contact:[email protected]",

author = "Danny Arends and Pjotr Prins and Jansen, {Ritsert C.} and Broman, {Karl W.}",

year = "2010",

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language = "English",

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TY - JOUR

T1 - R/qtl: high-throughput multiple QTL mapping

AU - Arends, Danny

AU - Prins, Pjotr

AU - Jansen, Ritsert C.

AU - Broman, Karl W.

PY - 2010/10/1

Y1 - 2010/10/1

N2 - Motivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.Contact:[email protected]

AB - Motivation: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10 000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis–trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets.Availability: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/.Contact:[email protected]

U2 - 10.1093/bioinformatics/btq565

DO - 10.1093/bioinformatics/btq565

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VL - 26

SP - 2990

EP - 2992

JO - Bioinformatics

JF - Bioinformatics

IS - 23

ER -

R/qtl: high-throughput multiple QTL mapping

Abstract

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Research output

High-throughput computational methods and software for quantitative trait locus (QTL) mapping

Integrative genomic approach identifies multiple genes involved in cardiac collagen deposition

Identifying genotype-by-environment interactions in the metabolism of germinating arabidopsis seeds using generalized genetical genomics

Activities

Novel Methods in Quantitative Trait Analysis (QTL)

Cite this