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.
Bioconductor version: Release (3.4)
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 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")
HTML | R Script | ChAMP: The Chip Analysis Methylation Pipeline |
Reference Manual | ||
Text | NEWS |
biocViews | CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel |
Version | 2.6.4 |
In Bioconductor since | BioC 2.13 (R-3.0) (3.5 years) |
License | GPL-3 |
Depends | R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest |
Imports | sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, GenomicRanges, RefFreeEWAS, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats |
LinkingTo | |
Suggests | knitr, rmarkdown |
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_2.6.4.tar.gz |
Windows Binary | ChAMP_2.6.4.zip |
Mac OS X 10.9 (Mavericks) | ChAMP_2.6.4.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/ChAMP/tree/release-3.4 |
Package Short Url | http://bioconductor.org/packages/ChAMP/ |
Package Downloads Report | Download Stats |
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