RnBeads

DOI: 10.18129/B9.bioc.RnBeads    

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

RnBeads

Bioconductor version: Development (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
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")

 

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

Details

biocViews	BatchEffect, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, MethylationArray, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version	2.17.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 years)
License	GPL-3
Depends	R (>= 3.0.0), BiocGenerics, S4Vectors(>= 0.9.25), GenomicRanges, MASS, cluster, ff, fields, ggplot2 (>= 0.9.2), gplots, grid, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr
Imports	IRanges
LinkingTo
Suggests	Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RnBeads.hg19, RnBeads.mm9, 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, MethylSeekR, sesame
SystemRequirements
Enhances
URL
Depends On Me	MAGAR
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_2.17.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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