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Bioinformatics. 2014 May 15;30(10):1484-5. doi: 10.1093/bioinformatics/btu028. Epub 2014 Jan 21.

CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.

Author information

1
Computational Biology and Data Mining Group, Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany, Graduate School of Life Sciences, Utrecht University, Universiteitsweg 98, 3584 CG, Utrecht, the Netherlands and Roche Diagnostics GmbH, 82377 Penzberg, Germany.

Abstract

SUMMARY:

The current methods available to detect chromosomal abnormalities from DNA microarray expression data are cumbersome and inflexible. CAFE has been developed to alleviate these issues. It is implemented as an R package that analyzes Affymetrix *.CEL files and comes with flexible plotting functions, easing visualization of chromosomal abnormalities.

AVAILABILITY AND IMPLEMENTATION:

CAFE is available from https://bitbucket.org/cob87icW6z/cafe/ as both source and compiled packages for Linux and Windows. It is released under the GPL version 3 license. CAFE will also be freely available from Bioconductor.

CONTACT:

sander.h.bollen@gmail.com or nancy.mah@mdc-berlin.de

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
24451624
PMCID:
PMC4016701
DOI:
10.1093/bioinformatics/btu028
[Indexed for MEDLINE]
Free PMC Article

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