RnBeads

DOI: 10.18129/B9.bioc.RnBeads    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RnBeads.

RnBeads

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RnBeads")

For older versions of R, please refer to the appropriate Bioconductor release.

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, ImmunoOncology, MethylSeq, MethylationArray, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version 2.2.0
In Bioconductor since BioC 3.1 (R-3.2) (4.5 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, qvalue, 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
Links To Me
Build Report  

Package Archives

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

Source Package RnBeads_2.2.0.tar.gz
Windows Binary RnBeads_2.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) RnBeads_2.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RnBeads
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RnBeads
Package Short Url https://bioconductor.org/packages/RnBeads/
Package Downloads Report Download Stats

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