methyAnalysis

DNA methylation data analysis and visualization

Bioconductor version: Release (2.14)

The methyAnalysis package aims for the DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focus on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.

Author: Pan Du, Richard Bourgon

Maintainer: Pan Du <dupan.mail at gmail.com>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("methyAnalysis")

To cite this package in a publication, start R and enter:

    citation("methyAnalysis")

Documentation

PDF R Script An Introduction to the methyAnalysis package
PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, Microarray, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 2.11 (R-2.15)
License Artistic-2.0
Depends R (>= 2.10), grid, IRanges, GenomicRanges, Biobase(>= 2.5.5), org.Hs.eg.db
Imports lumi, methylumi, Gviz, genoset, GenomicRanges, IRanges, rtracklayer, GenomicFeatures, annotate, Biobase(>= 2.5.5), AnnotationDbi, genefilter, biomaRt, methods
Suggests FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene
System Requirements
URL
Depends On Me
Imports Me
Suggests Me methylumi

Package Downloads

Package Source methyAnalysis_1.6.0.tar.gz
Windows Binary methyAnalysis_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) methyAnalysis_1.6.0.tgz
Mac OS X 10.9 (Mavericks)
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