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.
ChAMP
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see ChAMP.
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
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")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChAMP")
Documentation
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 |
Details
| 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 |
Package Archives
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
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
