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RnBeads

RnBeads


Bioconductor version: Release (3.18)

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")):

Installation

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


if (!require("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")
Comprehensive DNA Methylation Analysis with RnBeads PDF R Script
RnBeads Annotation PDF R Script
Reference Manual PDF
README Text
NEWS Text

Details

biocViews BatchEffect, CpGIsland, DNAMethylation, DataImport, DifferentialMethylation, Epigenetics, ImmunoOncology, MethylSeq, MethylationArray, Preprocessing, QualityControl, Sequencing, Software, TwoChannel
Version 2.20.0
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
URL
See More
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, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit, MethylSeekR, sesame
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

Package Archives

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

Source Package RnBeads_2.20.0.tar.gz
Windows Binary RnBeads_2.20.0.zip (64-bit only)
macOS Binary (x86_64) RnBeads_2.20.0.tgz
macOS Binary (arm64) RnBeads_2.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RnBeads
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RnBeads
Bioc Package Browser https://code.bioconductor.org/browse/RnBeads/
Package Short Url https://bioconductor.org/packages/RnBeads/
Package Downloads Report Download Stats