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QTLBIM specifications

Information


Unique identifier OMICS_07092
Name QTLBIM
Alternative name QTL Bayesian Interval Mapping
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 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Publication for QTL Bayesian Interval Mapping

QTLBIM citations

 (11)
library_books

Action of multiple intra QTL genes concerted around a co localized transcription factor underpins a large effect QTL

2015
Sci Rep
PMCID: 4623671
PMID: 26507552
DOI: 10.1038/srep15183

[…] higher number of Way Rarem alleles along qDTY12.1 corresponded with a higher yield under drought (). This result supported a role for multiple qDTY12.1 genes in yield under drought. Bayesian MCMC (R/qtlbim) analysis of this data fractionated qDTY12.1 into 4 regions () and suggested genes underlying the four LOD peaks as the four putative candidate genes; an amidohydrolase, a nodulin/SWEET13, no-a […]

library_books

Two Stage Genome Wide Search for Epistasis with Implementation to Recombinant Inbred Lines (RIL) Populations

2014
PLoS One
PMCID: 4275240
PMID: 25536193
DOI: 10.1371/journal.pone.0115680

[…] ed markers neighboring each of the framework markers identified in the first step. The proposed approach was compared to the Bayesian model selection approach of . The method is implemented using the qtlbim R package . We used the prior inclusion probability for epistasis defined in (12) in accordance with the simulated number of main effects in addition to epistasis. Probability of 0.5 was used f […]

call_split

Mixed effects models for GAW18 longitudinal blood pressure data

2014
BMC Proc
PMCID: 4143717
PMID: 25519345
DOI: 10.1186/1753-6561-8-S1-S87
call_split See protocol

[…] the positive truncated normal density with mean μ0 and variance σ02, and both mg0 and sg02 are prespecified hyperparameters. The proposed method has been implemented upon the widely used R package, R/qtlbim [] for these GAW18 longitudinal data. […]

library_books

Parametric and Nonparametric Statistical Methods for Genomic Selection of Traits with Additive and Epistatic Genetic Architectures

2014
PMCID: 4065247
PMID: 24727289
DOI: 10.1534/g3.114.010298

[…] For the purpose of illustrating the parametric and nonparametric prediction approaches, simulated data were created by the R () package QTL Bayesian interval mapping (“qtlbim”) (). R can be downloaded from http://www.r-project.org, the qtlbim package can be accessed by library(qtlbim) in R, and the description of the package can be fo […]

call_split

Genetic Architecture of Flowering Time Variation in Arabidopsis thaliana

2011
Genetics
PMCID: 3122318
PMID: 21406681
DOI: 10.1534/genetics.111.126607
call_split See protocol

[…] each parental allele, was gathered using the sim.geno, makeqtl, fitqtl, effectplot, and effectscan functions. Epistatic interactions between QTL were identified by using the qb.scantwo function in R/qtlbim ().For joint QTL analysis, all F2 plants were combined into a single population, the genotype of each chromosome at any given SNP taking on 1 of the 18 possible identities (from our founding ac […]

library_books

Characterisation of the macrophage transcriptome in glomerulonephritis susceptible and resistant rat strains

2010
Genes Immun
PMCID: 3048856
PMID: 21179115
DOI: 10.1038/gene.2010.61

[…] To calculate 1.5-LOD support interval estimates, data from the original genome screen for NTN susceptibility loci in F2 rats was re-analysed using the CRAN package R/qtlbim v1.9.4 . […]

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QTLBIM institution(s)
Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA

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