RnBeads
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see RnBeads.
RnBeads
Bioconductor version: 3.12
RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.
Author: Yassen Assenov [aut], Pavlo Lutsik [aut], Michael Scherer [aut], Fabian Mueller [aut, cre]
Maintainer: Fabian Mueller <rnbeads at mpi-inf.mpg.de>
citation("RnBeads")):
Installation
To install this package, start R (version "4.0") 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 | 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 | 2.8.1 |
| 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, gridExtra, limma, matrixStats, methods, illuminaio, methylumi, plyr |
| Imports | IRanges |
| System Requirements | |
| URL |
See More
| Suggests | Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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_2.8.1.tar.gz |
| Windows Binary | RnBeads_2.8.1.zip |
| macOS 10.13 (High Sierra) | RnBeads_2.8.1.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 |
| Old Source Packages for BioC 3.12 | Source Archive |