RnBeads : RnBeads

Package: RnBeads
Title: RnBeads
Description: RnBeads facilitates comprehensive analysis of various types of DNA
methylation data at the genome scale.
Authors@R: c(
person("Yassen", "Assenov", email = "yassen@mpi-inf.mpg.de",
role = c("aut")),
person("Pavlo", "Lutsik", email = "p.lutsik@mx.uni-saarland.de",
role = c("aut")),
person("Fabian", "Mueller", email = "rnbeads@mpi-inf.mpg.de",
role = c("aut", "cre")))
Date: 2016-03-20
Version: 1.4.0
Suggests: Category, GEOquery, GOstats, Gviz,
IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS,
RnBeads.hg19, 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, sva,
wateRmelon, wordcloud, argparse, glmnet, impute
Depends: R (>= 3.0.0), BiocGenerics, S4Vectors (>= 0.9.25),
GenomicRanges, MASS, RColorBrewer, cluster, ff, fields, ggplot2
(>= 0.9.2), gplots, gridExtra, limma, matrixStats, methods,
illuminaio, methylumi, plyr
Imports: IRanges
License: GPL-3
biocViews: DNAMethylation, MethylationArray, MethylSeq, Epigenetics,
QualityControl, Preprocessing, BatchEffect,
DifferentialMethylation, Sequencing, CpGIsland, TwoChannel,
DataImport
Collate: 'CNV.R' 'Report-class.R' 'Report-methods.R'
'ReportPlot-class.R' 'ReportPlot-methods.R'
'RnBDiffMeth-class.R' 'bigFf.R' 'RnBSet-class.R'
'RnBeadSet-class.R' 'RnBeadRawSet-class.R' 'RnBeads-package.R'
'RnBiseqSet-class.R' 'annotations.R' 'batch.R'
'batch.quality.R' 'bmiq.R' 'cellTypeAdjustment.R'
'clusterArchitecture.R' 'clusterArchitectureSGE.R'
'clustering.R' 'computeCluster.R' 'controlPlots.R'
'controlPlotsBiSeq.R' 'dataExport.R' 'dataImport.R'
'differentialMethylation.R' 'enrichment.R' 'filtering.R'
'filteringSummary.R' 'gender.R' 'greedycut.R' 'loading.R'
'logger.R' 'main.R' 'normalization.R' 'options.R'
'parallelProcessing.R' 'plottingUtils.R' 'profiles.R'
'qualityControl.R' 'readGEO.R' 'regionDescription.R'
'regionProfiles.R' 'subSegments.R' 'sva.R' 'utilities.R'
'wbcInference.R' 'agePrediction.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 06:18:43 UTC; biocbuild
Author: Yassen Assenov [aut],
Pavlo Lutsik [aut],
Fabian Mueller [aut, cre]
Maintainer: Fabian Mueller <rnbeads@mpi-inf.mpg.de>