RnBeads

DOI: 10.18129/B9.bioc.RnBeads    

RnBeads

Bioconductor version: Release (3.6)

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

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

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

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	1.10.8
In Bioconductor since	BioC 3.1 (R-3.2) (3 years)
License	GPL-3
Depends	R (>= 3.0.0), BiocGenerics, S4Vectors(>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr
Imports	IRanges
LinkingTo
Suggests	Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, RnBeads.hg19, 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, qvalue, sva, wateRmelon, wordcloud, argparse, glmnet, GLAD, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me	RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5
Build Report

Package Archives

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

Source Package	RnBeads_1.10.8.tar.gz
Windows Binary	RnBeads_1.10.8.zip
Mac OS X 10.11 (El Capitan)	RnBeads_1.10.8.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RnBeads
Package Short Url	http://bioconductor.org/packages/RnBeads/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive