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
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Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Bioconductor version: Release (3.5)
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")):
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
| HTML | R Script | ChAMP: The Chip Analysis Methylation Pipeline |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel |
| Version | 2.8.9 |
| In Bioconductor since | BioC 2.13 (R-3.0) (4 years) |
| License | GPL-3 |
| Depends | R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest |
| Imports | 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 |
| LinkingTo | |
| Suggests | knitr, rmarkdown |
| 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.
| Source Package | ChAMP_2.8.9.tar.gz |
| Windows Binary | ChAMP_2.8.9.zip |
| Mac OS X 10.11 (El Capitan) | ChAMP_2.8.9.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChAMP |
| Package Short Url | http://bioconductor.org/packages/ChAMP/ |
| Package Downloads Report | Download Stats |
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