charm
Analysis of DNA methylation data from CHARM microarrays
Bioconductor version: 2.10
This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.
Author: Martin Aryee, Peter Murakami, Harris Jaffee, Rafael Irizarry
Maintainer: Martin Aryee <aryee at jhu.edu>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("charm")
To cite this package in a publication, start R and enter:
citation("charm")
Documentation
| R Script | charm Vignette | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Bioinformatics, DNAMethylation, Microarray, Software |
| Depends | R (>= 2.14.0), Biobase, SQN, fields, RColorBrewer, genefilter |
| Imports | BSgenome, Biobase, oligo(>= 1.11.31), oligoClasses(>= 1.17.39), ff, preprocessCore, methods, stats, Biostrings, IRanges, siggenes, nor1mix, gtools, grDevices, graphics, utils, limma, parallel, sva(>= 3.1.2) |
| Suggests | charmData, BSgenome.Hsapiens.UCSC.hg18 |
| System Requirements | |
| License | LGPL (>= 2) |
| URL | |
| Depends On Me | charmData |
| Imports Me | |
| Suggests Me | |
| Version | 2.2.0 |
| Since | Bioconductor 2.6 (R-2.11) |
Package Downloads
| Package Source | charm_2.2.0.tar.gz |
| Windows Binary | charm_2.2.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | charm_2.2.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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