ChAMP

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450

Bioconductor version: Release (2.14)

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

Author: Tiffany Morris, Lee Butcher, Andy Feber, Andrew Teschendorff, Ankur Chakravarthy and Stephan Beck

Maintainer: Tiffany Morris <Tiffany.Morris at ucl.ac.uk>

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("ChAMP")

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

Documentation

PDF R Script Package
PDF   Reference Manual

Details

biocViews CopyNumber, MethylationArray, Microarray, Normalization, Software, TwoChannel
Version 1.2.7
In Bioconductor since BioC 2.13 (R-3.0)
License GPL-3
Depends R (>= 3.0.1), minfi, ChAMPdata, Illumina450ProbeVariants.db
Imports sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source ChAMP_1.2.7.tar.gz
Windows Binary ChAMP_1.2.7.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ChAMP_1.2.7.tgz
Mac OS X 10.9 (Mavericks) ChAMP_1.2.7.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center