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: 3.0
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 [cre, aut], Lee Butcher [aut], Andrew Feber [aut], Andrew Teschendorff [aut], Ankur Chakravarthy [aut]
Maintainer: Tiffany Morris <champ450k at gmail.com>
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 | 1.4.1 |
| 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 |
| 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_1.4.1.tar.gz |
| Windows Binary | ChAMP_1.4.1.zip |
| Mac OS X 10.6 (Snow Leopard) | ChAMP_1.4.1.tgz |
| Mac OS X 10.9 (Mavericks) | ChAMP_1.4.1.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
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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