RnBeads
This is thereleased version of RnBeads; for the devel version, seeRnBeads.
RnBeads
Bioconductor version: Release (3.22)
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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("RnBeads")For older versions of R, please refer to the appropriateBioconductor 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 | 2.28.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (10.5 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,reshape2 |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | RnBeads_2.28.0.tar.gz |
| Windows Binary (x86_64) | RnBeads_2.27.2.zip |
| macOS Binary (x86_64) | RnBeads_2.28.0.tgz |
| macOS Binary (arm64) | RnBeads_2.28.0.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 |