RnBeads
This is the development version of RnBeads; for the stable release version, see RnBeads.
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 rnbeads.org>
citation("RnBeads")
):
Installation
To install this package, start R (version "4.4") 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")
Comprehensive DNA Methylation Analysis with RnBeads | R Script | |
RnBeads Annotation | R Script | |
Reference Manual | ||
README | Text | |
NEWS | Text |
Details
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) (9.5 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 |
System Requirements | |
URL |
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, 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_2.23.0.tar.gz |
Windows Binary | RnBeads_2.23.0.zip |
macOS Binary (x86_64) | RnBeads_2.23.0.tgz |
macOS Binary (arm64) | RnBeads_2.23.0.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 |