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.

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")):

To install this package, start R and enter:

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

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

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

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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