RnBeads

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

RnBeads

Bioconductor version: Development (3.24)

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 rnbeads.org>

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

Yassen Assenov, Christoph Bock, Pavlo Lutsik, Michael Scherer, Fabian Mueller. RnBeads: RnBeads. doi:10.18129/B9.bioc.RnBeads, R package version 2.31.2, https://bioconductor.org/packages/RnBeads.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BatchEffect, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, MethylationArray, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version	2.31.2
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	GPL-3
Depends	R (>= 4.1.0), BiocGenerics, S4Vectors (>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr, reshape2
Imports	IRanges, ComplexHeatmap
System Requirements
URL

Suggests	Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, RnBeads.hg38, 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, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame, dplyr
Linking To
Enhances
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, r-universe

Package Archives

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

Source Package	RnBeads_2.31.2.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)	RnBeads_2.31.2.tgz
macOS Binary (sonoma-arm64)	RnBeads_2.31.1.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