To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("ChAMP")
In most cases, you don't need to download the package archive at all.
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ChAMP.
Bioconductor version: 3.3
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. In addition there is a method to help calculate hmC using BS and oxBS samples.
Author: Tiffany Morris [cre, aut], Yuan Tian [aut], Lee Stirling [ctb], Andrew Feber [ctb], Andrew Teschendorff [ctb], Ankur Chakravarthy [ctb]
Maintainer: Yuan Tian, Tiffany Morris <champ450k at gmail.com>
Citation (from within R,
enter citation("ChAMP")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("ChAMP")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChAMP")
R Script | The \Rpackage{ChAMP} Package | |
Reference Manual | ||
Text | NEWS |
biocViews | CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel |
Version | 1.10.0 |
In Bioconductor since | BioC 2.13 (R-3.0) (3 years) |
License | GPL-3 |
Depends | R (>= 3.2), minfi, ChAMPdata, Illumina450ProbeVariants.db |
Imports | sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, GenomicRanges, RefFreeEWAS, qvalue, isva, doParallel, bumphunter, quadprog |
LinkingTo | |
Suggests | |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | ChAMP_1.10.0.tar.gz |
Windows Binary | ChAMP_1.10.0.zip |
Mac OS X 10.9 (Mavericks) | ChAMP_1.10.0.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/ChAMP/tree/release-3.3 |
Package Short Url | http://bioconductor.org/packages/ChAMP/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: