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DESCRIPTION
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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 = "[email protected]",
role = c("aut")),
person("Christoph", "Bock", email = "[email protected]",
role = c("aut")),
person("Pavlo", "Lutsik", email = "[email protected]",
role = c("aut")),
person("Michael", "Scherer", email = "[email protected]",
role = c("aut")),
person("Fabian", "Mueller", email = "[email protected]",
role = c("aut", "cre")))
Date: 2023-08-01
Version: 2.19.0
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
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
License: GPL-3
biocViews: DNAMethylation, MethylationArray, MethylSeq, Epigenetics,
QualityControl, Preprocessing, BatchEffect, DifferentialMethylation,
Sequencing, CpGIsland, ImmunoOncology, 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'
'agePrediction.R'
'annotations.R'
'batch.R'
'batch.quality.R'
'bmiq.R'
'cellTypeAdjustment.R'
'clusterArchitecture.R'
'clusterArchitectureSGE.R'
'clusterArchitectureSLURM.R'
'clustering.R'
'combining.R'
'computeCluster.R'
'controlPlots.R'
'controlPlotsBiSeq.R'
'dataExport.R'
'dataImport.R'
'differentialMethylation.R'
'differentialVariability.R'
'enmix.R'
'enrichment.R'
'exportGEO.R'
'filtering.R'
'filteringSummary.R'
'genomewide.R'
'greedycut.R'
'immune.R'
'loading.R'
'logger.R'
'lolaUtils.R'
'main.R'
'normalization.R'
'normalizationMethods.R'
'options.R'
'parallelProcessing.R'
'plottingUtils.R'
'profiles.R'
'qualityControl.R'
'readGEO.R'
'regionDescription.R'
'regionProfiles.R'
'segmentation.R'
'sesame.R'
'sex.R'
'subSegments.R'
'sva.R'
'utilities.R'
'wbcInference.R'
RoxygenNote: 7.1.2