Bioinformatics. 2010 Jan 1;26(1):134-5. Epub 2009 Oct 22.

The gputools package enables GPU computing in R.

Buckner J, Wilson J, Seligman M, Athey B, Watson S, Meng F.

Source

Department of Psychiatry and Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA. bucknerj@umich.edu

Abstract

MOTIVATION:

By default, the R statistical environment does not make use of parallelism. Researchers may resort to expensive solutions such as cluster hardware for large analysis tasks. Graphics processing units (GPUs) provide an inexpensive and computationally powerful alternative. Using R and the CUDA toolkit from Nvidia, we have implemented several functions commonly used in microarray gene expression analysis for GPU-equipped computers.

RESULTS:

R users can take advantage of the better performance provided by an Nvidia GPU.

AVAILABILITY:

The package is available from CRAN, the R project's repository of packages, at http://cran.r-project.org/web/packages/gputools More information about our gputools R package is available at http://brainarray.mbni.med.umich.edu/brainarray/Rgpgpu

PMID:: 19850754; [PubMed - indexed for MEDLINE]
PMCID:: PMC2796814

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Research Support, N.I.H., Extramural

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Grant Support

1U54DA021519-01A1/DA/NIDA NIH HHS/United States

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