To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChAMP")
In most cases, you don't need to download the package archive at all.
ChAMP
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450
Bioconductor version: 2.14
The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number aberrations.
Author: Tiffany Morris, Lee Butcher, Andy Feber, Andrew Teschendorff, Ankur Chakravarthy and Stephan Beck
Maintainer: Tiffany Morris <Tiffany.Morris at ucl.ac.uk>
Citation (from within R,
enter citation("ChAMP")):
Installation
To install this package, start R and enter:
source("http://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 | Package | |
| Reference Manual |
Details
| biocViews | CopyNumber, MethylationArray, Microarray, Normalization, Software, TwoChannel |
| Version | 1.2.8 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-3 |
| Depends | R (>= 3.0.1), minfi, ChAMPdata, Illumina450ProbeVariants.db |
| Imports | sva, IlluminaHumanMethylation450kmanifest, limma, RPMM, DNAcopy, preprocessCore, impute, marray, wateRmelon, plyr |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ChAMP_1.2.8.tar.gz |
| Windows Binary | ChAMP_1.2.8.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | ChAMP_1.2.8.tgz |
| Mac OS X 10.9 (Mavericks) | ChAMP_1.2.8.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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