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

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, e...

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Bibliographic Details
Published inBioinformatics Vol. 30; no. 10; pp. 1484 - 1485
Main Authors Bollen, Sander, Leddin, Mathias, Andrade-Navarro, Miguel A., Mah, Nancy
Format Journal Article
LanguageEnglish
Published England Oxford University Press 15.05.2014
Subjects
Abnormalities
Applications Notes
Bioinformatics
Chromosome Aberrations
Deoxyribonucleic acid
Gene Expression
Markov Chains
Oligonucleotide Array Sequence Analysis - methods
Packages
Plotting
Software
Summaries
Visualization
Online AccessGet full text
ISSN1367-4803
1367-4811
1460-2059
1367-4811
DOI10.1093/bioinformatics/btu028

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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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Associate Editor: Janet Kelso
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btu028