R/qtl protocols

View R/qtl computational protocol

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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 1.42-8
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Karl W. Broman <>

Additional information


https://github.com/kbroman/qtl/issues http://www.rqtl.org/

Publications for R/qtl

R/qtl in pipelines

 (18)
2017
PMCID: 5437220
PMID: 28580001
DOI: 10.3389/fpls.2017.00828

[…] used for its speed and robustness against non-normality (). the confidence interval for each qtl peak was derived from the bayesian 95% credible interval using the bayesint function implemented in r/qtl. all the qtls detected were named as follows: ebwr ‘linkage group number’ (ebwr, the acronym for eggplant bacterial wilt resistance)., the itag2.4 tomato annotated transcriptome () […]

2017
PMCID: 5496852
PMID: 28676627
DOI: 10.1038/s41598-017-04609-5

[…] http://phytozome.jgi.doe.gov/), using bwa, and indel realignment and joint variant calling were performed with the gatk using the naive pipeline of the rig workflow–. qtl mapping was performed in r/qtl using interval mapping (im) with 1000 permutations and an α = 0.05. both the genetic map and qtl mapping were performed as an f7 instead of a ril population due to excess heterozygosity., mqm […]

2017
PMCID: 5608495
PMID: 28671645
DOI: 10.3791/55185

[…]  of the me49-fudrr x vand-snfr cross were assessed for resistance to the drug sinefungin as described in protocol 1. using the genetic map and the snfr phenotype of the progeny, a qtl scan was run in r/qtl - protocol 2 (figure 2). this resulted in one significant peak on chromosome ix spanning approximately 1 mbp. it is in this region that the causal mutation is located., to identify the causal mu […]

2017
PMCID: 5608495
PMID: 28671645
DOI: 10.3791/55185

[…] snfr gene using the me49-fudrr x vand-snfr cross are shown with reference to the appropriate protocols outlined in this article. please click here to view a larger version of this figure., figure 2: r/qtl commands to run qtl scan on the snfr phenotype. the commands as outlined in protocol 2 were run in r using the qtl package. representative commands and plot are shown. please click here to view […]

2017
PMCID: 5654460
PMID: 29085243
DOI: 10.1270/jsbbs.17007

[…] data, low-quality snps (read depth <6 or >5 missing data per locus) were filtered. after filtering, 2,522 snps were retained for the 37 bc2f4 individuals. linkage analysis involved use of the r/qtl package (). the snp positions in this study are based on the msu rice genome annotation project database release 7 (http://rice.plantbiology.msu.edu/) ()., raw rad-seq reads for two parents […]


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R/qtl in publications

 (487)
PMCID: 5919379
PMID: 29698431
DOI: 10.1371/journal.pone.0196148

[…] autosomal snps using the illumina medium density linkage panel. additional details regarding the genotyping and phenotyping are available []., we used haley-knott regression [] as implemented in r/qtl [] to identify qtls for our phenotypes. the genome-wide significance threshold was determined using a permutation test based on 10000 replicates []. we intersected the mouse qtl results […]

PMCID: 5905146
PMID: 29665794
DOI: 10.1186/s12870-018-1267-8

[…] qtl detected for selfed seed set in 38% of the runs. the qtl for plant height on lg 4 was found in 69% of the runs. we verified the qtl analysis with a single marker regression model implemented in r/qtl to confirm the multiple regression model used within plabmqtl. both algorithms identified the qtl at the same positions, and had very similar proportions of phenotypic variances explained., […]

PMCID: 5895046
PMID: 29601575
DOI: 10.1371/journal.pntd.0006368

[…] of n2 and cb4856 [, ], as well as 153 unique c. briggsae recombinant inbred lines (rils) created using af16 and hk104 []. these phenotypic data were collected and processed as described above. r/qtl [] was used to carry out marker regression on 1454 c. elegans markers and 1031 c. briggsae markers. qtl were detected by calculating logarithm of odds (lod) scores for each marker […]

PMCID: 5947151
PMID: 29574807
DOI: 10.1111/nph.15089

[…] caused by well position and sample weight. the command data=convert2riself(mydata) was used to include the algorithm for the investigation of a ril population during the qtl analysis using the r/qtl program. standard interval mapping was performed using a genome‐wide scan for the identification of loci. the significant threshold was determined using a 1000‐replicate permutation test […]

PMCID: 5861201
PMID: 29593772
DOI: 10.3389/fpls.2018.00322

[…] used and for previously published traits, reported trait values were used (supplementary dataset ). the core ril 99 markers were downloaded from tair (supplementary dataset ). for each trait, the r/qtl () scanone function we used with the imputation method and a walking speed of 1 cm. we performed 10,000 iterations to determine genome-wide lod (log10 of odds) score significance thresholds […]


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R/qtl institution(s)
Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA; Department of Horticulture, University of Wisconsin-Madison, Madison, WI, USA; Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA; 23andMe, Mountain View, CA, USA; The Jackson Laboratory, Bar Harbor, ME, USA; Department of Genetics, Genomics, and Informatics, University of Tennessee Health Sciences Center, Memphis, TN, USA; Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA; Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
R/qtl funding source(s)
Supported in part by National Institutes of Health grants R01GM074244, R01GM070683, and R01GM123489.

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