To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RnBeads")

In most cases, you don't need to download the package archive at all.

RnBeads

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see RnBeads.

RnBeads

Bioconductor version: 3.1

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Author: Yassen Assenov [aut], Pavlo Lutsik [aut], Fabian Mueller [aut, cre]

Maintainer: Fabian Mueller <rnbeads at mpi-inf.mpg.de>

Citation (from within R, enter citation("RnBeads")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RnBeads")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("RnBeads")
PDF R Script Comprehensive DNA Methylation Analysis with RnBeads
PDF R Script RnBeads Annotation
PDF Reference Manual
Text README
Text NEWS

Details

biocViews BatchEffect, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, MethylSeq, MethylationArray, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version 1.0.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License GPL-3
Depends R (>= 3.0.0), BiocGenerics, GenomicRanges, MASS, RColorBrewer, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr
Imports IRanges
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Rnorvegicus.UCSC.rn5, Category, GEOquery, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, RnBeads.hg19, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, sva, wateRmelon, wordcloud, argparse
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me RnBeads.hg19, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source RnBeads_1.0.0.tar.gz
Windows Binary RnBeads_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) RnBeads_1.0.0.tgz
Mac OS X 10.9 (Mavericks) RnBeads_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/RnBeads/tree/release-3.1
Package Short Url http://bioconductor.org/packages/RnBeads/
Package Downloads Report Download Stats

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