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Bioinformatics Advance Access originally published online on April 5, 2009
Bioinformatics 2009 25(11):1447-1448; doi:10.1093/bioinformatics/btp169
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x

Vincent J. Carey 1,*, Adam R. Davis 2, Michael F. Lawrence 3, Robert Gentleman 3 and Benjamin A. Raby 1

1Channing Laboratory, Department of Medicine, 2I2B2 National Center for Biocomputing, Brigham and Women's Hospital, 75 Francis St. Boston MA 02115 and 3Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA.

*To whom correspondence should be addressed.


  Abstract

Summary: Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these associations. This work is motivated by emerging requirements for data architectures and algorithm interfaces to allow flexible exploration of public and private archives of genotyping and expression arrays. Using R/Bioconductor facilities, Phase II HapMap genotypes and Illumina 47K expression assay results archived on multiple populations may be interactively explored and analyzed using commodity hardware.

Availability and Implementation: Open Source. Bioconductor 2.3 packages GGtools, GGBase, GGdata, hmyriB36. Freely available on the web at http://www.bioconductor.org

Contact: stvjc{at}channing.harvard.edu

Associate Editor: Alex Bateman

Received on January 5, 2009; revised on February 27, 2009; accepted on March 19, 2009

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