DOI: 10.18129/B9.bioc.ChAMP    

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Bioconductor version: Release (3.6)

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

Author: Yuan Tian [cre,aut], Tiffany Morris [ctb], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb]

Maintainer: Yuan Tian <champ450k at>

Citation (from within R, enter citation("ChAMP")):


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HTML R Script ChAMP: The Chip Analysis Methylation Pipeline
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biocViews CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 2.9.10
In Bioconductor since BioC 2.13 (R-3.0) (4.5 years)
License GPL-3
Depends R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest
Imports prettydoc, sva, illuminaio, rmarkdown, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, missMethyl, GenomicRanges, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats, combinat
Suggests knitr, rmarkdown
Depends On Me
Imports Me
Suggests Me
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