ChAMP
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ChAMP.
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Bioconductor version: 3.9
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("ChAMP")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ChAMP")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChAMP")| ChAMP: The Chip Analysis Methylation Pipeline | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumber, DNAMethylation, MethylationArray, Microarray, Normalization, Software, TwoChannel |
| Version | 2.14.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.3), minfi, ChAMPdata(>= 2.6.0), FEM(>= 3.1), DMRcate, Illumina450ProbeVariants.db, IlluminaHumanMethylationEPICmanifest |
| Imports | prettydoc, Hmisc, globaltest, sva, illuminaio, rmarkdown, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr, goseq, missMethyl, kpmt, GenomicRanges, qvalue, isva, doParallel, bumphunter, quadprog, shiny, shinythemes, plotly (>= 4.5.6), RColorBrewer, dendextend, matrixStats, combinat |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChAMP_2.14.0.tar.gz |
| Windows Binary | ChAMP_2.14.0.zip |
| Mac OS X 10.11 (El Capitan) | ChAMP_2.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChAMP |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChAMP |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChAMP/ |
| Package Short Url | https://bioconductor.org/packages/ChAMP/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |