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This is the development version of RnBeads; for the stable release version, see RnBeads.


Bioconductor version: Development (3.20)

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

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

Maintainer: Fabian Mueller <team at>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


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

Comprehensive DNA Methylation Analysis with RnBeads PDF R Script
RnBeads Annotation PDF R Script
Reference Manual PDF


biocViews BatchEffect, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, MethylationArray, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version 2.23.0
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License GPL-3
Depends R (>= 3.0.0), BiocGenerics, S4Vectors(>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr
Imports IRanges
System Requirements
See More
Suggests Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme,,,, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame
Linking To
Depends On Me MAGAR
Imports Me
Suggests Me RnBeads.hg19, RnBeads.hg38, RnBeads.mm10, RnBeads.mm9, RnBeads.rn5
Links To Me
Build Report Build Report

Package Archives

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

Source Package RnBeads_2.23.0.tar.gz
Windows Binary
macOS Binary (x86_64) RnBeads_2.23.0.tgz
macOS Binary (arm64) RnBeads_2.23.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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