bsseq
Analyze, manage and store bisulfite sequencing data

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Functions
214
Source code
39
Man pages
25
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bsseq: Analyze, manage and store bisulfite sequencing data
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API

API for bsseq
Analyze, manage and store bisulfite sequencing data

Global functions
.BSmooth Source code
.areBackendsInMemory Source code
.bsGetCol Source code
.bsGetGr Source code
.bsHighlightRegions Source code
.bsPlotLines Source code
.bsPlotPoints Source code
.bsPlotTitle Source code
.checkAssayNames Source code
.checkMandCov Source code
.collapseColData Source code
.colsum Source code
.combineList Source code
.combineList_matrix Source code
.combineList_matrix_like Source code
.constructCounts Source code
.constructCountsFromSingleFile Source code
.contructFWGRangesFromBismarkFiles Source code
.findOverlaps_FWGRanges Source code
.getBSseqBackends Source code
.getRegionStats Source code
.getRegionStats_ttest Source code
.getSEDir Source code
.getSeedClasses Source code
.guessBismarkFileType Source code
.isHDF5ArrayBacked Source code
.isHDF5BackedBSseqUpdatable Source code
.isSimpleDelayedMatrix Source code
.isSingleMachineBackend Source code
.oldTrans Source code
.plotSmoothData Source code
.quantile Source code
.readBismarkAsDT Source code
.readBismarkAsFWGRanges Source code
.rowSds Source code
.rowTickmarks Source code
.rowVars Source code
.rowsum Source code
.set_FWIRanges_end Source code
.set_FWIRanges_start Source code
.set_FWIRanges_width Source code
.strandCollapse Source code
.valid.FWIRanges Source code
.zero_type Source code
BS.chr22 Man page
BSmooth Man page Source code
BSmooth.fstat Man page Source code
BSmooth.tstat Man page Source code
BSseq Man page Source code
BSseq-class Man page
BSseqStat Man page Source code
BSseqStat-class Man page
BSseqTstat Man page Source code
BSseqTstat-class Man page
FWGRanges-class Man page
FWIRanges-class Man page
[,BSseq-method Man page
[,BSseqStat,ANY,ANY,ANY-method Man page
[,BSseqStat-method Man page
[,BSseqTstat,ANY,ANY,ANY-method Man page
[,BSseqTstat-method Man page
[,hasGRanges,ANY,ANY,ANY-method Man page
[,hasGRanges-method Man page
assayNames,BSseq-method Man page
assays,BSseq-method Man page
binomialGoodnessOfFit Man page Source code
blockApplyWithRealization Source code
chisqGoodnessOfFit Man page
chrSelectBSseq Man page Source code
class:hasGRanges Man page
clusterMaker Source code
collapseBSseq Man page Source code
combine,BSseq,BSseq-method Man page
combineList Man page Source code
computeStat Man page Source code
data.frame2GRanges Man page Source code
dimnames,arrayRealizationSink-method Man page
dmrFinder Man page Source code
end,FWGRanges-method Man page
end,FWIRanges-method Man page
end,hasGRanges-method Man page
end<-,FWIRanges-method Man page
end<-,hasGRanges-method Man page
findLoci Man page Source code
findOverlaps,FWGRanges,FWGRanges-method Man page
findOverlaps,GenomicRanges,hasGRanges-method Man page
findOverlaps,hasGRanges,GenomicRanges-method Man page
findOverlaps,hasGRanges,hasGRanges-method Man page
fisherTests Man page Source code
fstat.comparisons.pipeline Source code
fstat.pipeline Source code
getBSseq Man page Source code
getCoverage Man page Source code
getFWER Source code
getFWER.fstat Source code
getMeth Man page Source code
getNullBlocks_BSmooth.tstat Source code
getNullDistribution_BSmooth.fstat Source code
getNullDistribution_BSmooth.tstat Source code
getNullDmrs_BSmooth.tstat Source code
getStats Man page Source code
getStats_BSseqStat Source code
getStats_BSseqTstat Source code
granges,hasGRanges-method Man page
hasBeenSmoothed Man page Source code
hasGRanges Man page
hasGRanges-class Man page
length,BSseq-method Man page
length,hasGRanges-method Man page
localCorrectStat Source code
makeClusters Source code
makeIdxMatrix Source code
matrixOrNULL-class Man page
names,FWIRanges-method Man page
names<-,FWIRanges-method Man page
orderBSseq Man page Source code
overlapsAny,GenomicRanges,hasGRanges-method Man page
overlapsAny,hasGRanges,GenomicRanges-method Man page
overlapsAny,hasGRanges,hasGRanges-method Man page
pData,BSseq-method Man page
pData<-,BSseq,DataFrame-method Man page
pData<-,BSseq,data.frame-method Man page
parsingPipeline Source code
permuteAll Source code
plot.BSseqTstat Source code
plot.chisqGoodnessOfFit Man page Source code
plotAnnoTrack Source code
plotGeneTrack Source code
plotManyRegions Man page Source code
plotRegion Man page Source code
poissonGoodnessOfFit Man page Man page Source code
print.chisqGoodnessOfFit Man page Source code
print.summary.BSseqTstat Source code
read.bismark Man page Source code
read.bsmooth Man page Source code
read.bsmoothDirRaw Source code
read.umtab Man page Source code
read.umtab.chr Source code
read.umtab2 Man page Source code
read.umtab2.chr Source code
read.umtab2.chr2 Source code
regionFinder3 Source code
sampleNames,BSseq-method Man page
sampleNames<-,BSseq,ANY-method Man page
sampleRawToBSseq Source code
seqlengths,hasGRanges-method Man page
seqlengths<-,hasGRanges-method Man page
seqlevels,hasGRanges-method Man page
seqlevels<-,hasGRanges-method Man page
seqnames,FWGRanges-method Man page
seqnames,hasGRanges-method Man page
seqnames<-,hasGRanges-method Man page
set_FWIRanges_names Source code
show,BSseq-method Man page
show,BSseqStat-method Man page
show,BSseqTstat-method Man page
smoothSds Man page Source code
start,FWGRanges-method Man page
start,FWIRanges-method Man page
start,hasGRanges-method Man page
start<-,FWIRanges-method Man page
start<-,hasGRanges-method Man page
strand,FWGRanges-method Man page
strand,hasGRanges-method Man page
strand<-,hasGRanges,ANY-method Man page
strand<-,hasGRanges-method Man page
strandCollapse Man page Source code
subsetBlocks Source code
subsetByOverlaps,GenomicRanges,hasGRanges-method Man page
subsetByOverlaps,hasGRanges,GenomicRanges-method Man page
subsetByOverlaps,hasGRanges,hasGRanges-method Man page
subsetDmrs Source code
summary.BSseqTstat Source code
updateObject,BSseq-method Man page
updateObject,BSseqStat-method Man page
updateObject,BSseqTstat-method Man page
width,FWGRanges-method Man page
width,FWIRanges-method Man page
width,hasGRanges-method Man page
width<-,FWIRanges-method Man page
width<-,hasGRanges-method Man page
bsseq documentation built on Nov. 8, 2020, 7:53 p.m.

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