R/qtl pipeline

R/qtl specifications

Information


Unique identifier OMICS_07093
Name R/qtl
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.41-6
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Karl W. Broman <>

Additional information


Homepage: http://www.rqtl.org/ Tutorials: http://www.rqtl.org/tutorials/

Publications for R/qtl

R/qtl IN pipelines

 (3)
2017
PMCID: 5716196
PMID: 29036322
DOI: 10.1093/nar/gkx853

[…] and the detection of bad markers was set to ‘yes’. the genotyping error of genetically mapped markers was estimated by determining the maximum likelihood from a range of potential errors using r/qtl (34)., genetic maps were also constructed from 70% mcr tgbs (grl2) filtered snp set for 192 b73 × mo17 f2 individuals using asmap. imputation and genetic mapping were performed as described […]

2016
PMCID: 5217118
PMID: 27866151
DOI: 10.1534/g3.116.035741

[…] mapping. parental allele assignment and imputation were performed using the window ld function of fsfhap (swarts et al. 2014) incorporated into tassel 5.0., linkage map construction was performed in r/qtl (r foundation for statistical computing) using the 2977 polymorphic, high-quality snp markers obtained from gbs (supplemental material, figure s1, file s1, file s2, and table 1). genetic […]

2015
PMCID: 5034846
PMID: 25845500
DOI: 10.1111/jipb.12358

[…] recombinants and recombinant‐derived f3 families at indel markers were electrophoretically determined on a 3% agarose gel., quantitative trait locus mapping was performed using a modified version of r/qtl, which takes into account the bc2s3 pedigree of the rils (shannon 2012). a previously described multiple qtl mapping procedure (shannon 2012) was used to identify qtl for vascular bundle […]

R/qtl institution(s)
Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands; Department of Nematology, Wageningen University, Wageningen, The Netherlands; Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
R/qtl funding source(s)
Supported by National Institutes of Health (GM074244), the Netherlands Organisation for Scientific Research/TTI Green Genetics (1CC029RP), the Centre for BioSystems Genomics (CBSG), the Netherlands Consortium of Systems Biology (NCSB), both of which are part of the Netherlands Genomics Initiative / Netherlands Organisation for Scientific Research and the EU 7th Framework Programme under the Research Project PANACEA (222936).

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