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

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 fun...

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Detalles Bibliográficos
Autores principales: Bollen, Sander, Leddin, Mathias, Andrade-Navarro, Miguel A., Mah, Nancy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016701/
https://www.ncbi.nlm.nih.gov/pubmed/24451624
http://dx.doi.org/10.1093/bioinformatics/btu028
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author Bollen, Sander
Leddin, Mathias
Andrade-Navarro, Miguel A.
Mah, Nancy
author_facet Bollen, Sander
Leddin, Mathias
Andrade-Navarro, Miguel A.
Mah, Nancy
author_sort Bollen, Sander
collection PubMed
description 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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spelling pubmed-40167012014-05-12 CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data Bollen, Sander Leddin, Mathias Andrade-Navarro, Miguel A. Mah, Nancy Bioinformatics Applications Notes 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. Oxford University Press 2014-05-15 2014-01-21 /pmc/articles/PMC4016701/ /pubmed/24451624 http://dx.doi.org/10.1093/bioinformatics/btu028 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Bollen, Sander
Leddin, Mathias
Andrade-Navarro, Miguel A.
Mah, Nancy
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
title CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
title_full CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
title_fullStr CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
title_full_unstemmed CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
title_short CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data
title_sort cafe: an r package for the detection of gross chromosomal abnormalities from gene expression microarray data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016701/
https://www.ncbi.nlm.nih.gov/pubmed/24451624
http://dx.doi.org/10.1093/bioinformatics/btu028
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