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Bioinformatics. 2014 Feb 1;30(3):428-30. doi: 10.1093/bioinformatics/btt684. Epub 2013 Dec 12.

ChAMP: 450k Chip Analysis Methylation Pipeline.

Author information

1
Medical Genomics, and Statistical Genomics, UCL Cancer Institute, University College London, London WC1E 6BT, UK, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Shanghai 200031, China and Institute of Environmental Medicine, Karolinska Instytutet, 17177 Stockholm, Sweden.

Abstract

The Illumina Infinium HumanMethylation450 BeadChip is a new platform for high-throughput DNA methylation analysis. Several methods for normalization and processing of these data have been published recently. Here we present an integrated analysis pipeline offering a choice of the most popular normalization methods while also introducing new methods for calling differentially methylated regions and detecting copy number aberrations.

AVAILABILITY AND IMPLEMENTATION:

ChAMP is implemented as a Bioconductor package in R. The package and the vignette can be downloaded at bioconductor.org

PMID:
24336642
PMCID:
PMC3904520
DOI:
10.1093/bioinformatics/btt684
[Indexed for MEDLINE]
Free PMC Article
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