title: iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.
abstract: BACKGROUND
  Recently, mapping studies of expression quantitative loci (eQTL) (where gene expression levels are viewed as quantitative traits) have provided insight into the biology of gene regulation. Bayesian methods provide natural modeling frameworks for analyzing eQTL studies, where information shared across markers and/or genes can increase the power to detect eQTLs. Bayesian approaches tend to be computationally demanding and require specialized software. As a result, most eQTL studies use univariate methods treating each gene independently, leading to suboptimal results.
  
  
  RESULTS
  We present a powerful, computationally optimized and free open-source R package, iBMQ. Our package implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently. Model parameters are estimated using a Markov chain Monte Carlo algorithm. The free and widely used openMP parallel library speeds up computation. Using a mouse cardiac dataset, we show that iBMQ improves the detection of large trans-eQTL hotspots compared with other state-of-the-art packages for eQTL analysis.
  
  
  BACKGROUND
  The R-package iBMQ is available from the Bioconductor Web site at http://bioconductor.org and runs on Linux, Windows and MAC OS X. It is distributed under the Artistic Licence-2.0 terms.
  
  
  BACKGROUND
  christian.deschepper@ircm.qc.ca or rgottard@fhcrc.org.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Statistics, University of Washington, Seattle, WA 98195, USA, Institut de recherches cliniques de Montréal and Université de Montréal, Montréal, Quebec, Canada H2W 1R7, Faculty of Medicine, Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada H3A 1A2 and Vaccine and Infections Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
authors: Greg C
authors: GC
authors: Imholte
authors: Marie-Pier
authors: MP
authors: Scott-Boyer
authors: Aurélie
authors: A
authors: Labbe
authors: Christian F
authors: CF
authors: Deschepper
authors: Raphael
authors: R
authors: Gottardo
mesh_terms: D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D015870:Gene Expression; D008390:Markov Chains; D051379:Mice; D009010:Monte Carlo Method; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012984:Software
references: G3 (Bethesda). 2013 Apr 9;3(4):597-605
references: 23550129
references: Bioinformatics. 2003 May 1;19(7):889-90
references: 12724300
references: Trends Genet. 2008 Aug;24(8):408-15
references: 18597885
references: Biostatistics. 2004 Apr;5(2):155-76
references: 15054023
references: Bioinformatics. 2009 Jun 1;25(11):1447-8
references: 19349284
references: Stat Appl Genet Mol Biol. 2012 Jul 12;11(4):
references: 22850063