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

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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.

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