+,BSFDataSet,BSFDataSet-method	add-BSFDataSet
add-BSFDataSet	add-BSFDataSet
annotateWithScore	annotateWithScore
assignToGenes	assignToGenes
assignToTranscriptRegions	assignToTranscriptRegions
bindingSiteCoveragePlot	bindingSiteCoveragePlot
bindingSiteDefinednessPlot	bindingSiteDefinednessPlot
BSFDataSet	BSFDataSet
BSFDataSet,	BSFDataSet
BSFDataSet-class,	BSFDataSet
BSFDataSetFromBigWig	BSFDataSet
BSFind	BSFind
calculateBsBackground	calculateBsBackground
calculateBsFoldChange	calculateBsFoldChange
calculateSignalToFlankScore	calculateSignalToFlankScore
clipCoverage	clipCoverage
collapseReplicates	collapseReplicates
combineBSF	combineBSF
coverageOverRanges	coverageOverRanges
duplicatedSitesPlot	duplicatedSitesPlot
estimateBsWidth	estimateBsWidth
estimateBsWidthPlot	estimateBsWidthPlot
exportTargetGenes	exportTargetGenes
exportToBED	exportToBED
filterBsBackground	filterBsBackground
geneOverlapsPlot	geneOverlapsPlot
getMeta	getMeta
getMeta,BSFDataSet-method	getMeta
getName	getName
getName,BSFDataSet-method	getName
getRanges	getRanges
getRanges,BSFDataSet-method	getRanges
getSignal	getSignal
getSignal,BSFDataSet-method	getSignal
getSummary	getSummary
getSummary,BSFDataSet-method	getSummary
globalScorePlot	globalScorePlot
imputeBsDifferencesForTestdata	imputeBsDifferencesForTestdata
makeBindingSites	makeBindingSites
makeBsSummaryPlot	makeBsSummaryPlot
mergeCrosslinkDiagnosticsPlot	mergeCrosslinkDiagnosticsPlot
mergeSummaryPlot	mergeSummaryPlot
plotBsBackgroundFilter	plotBsBackgroundFilter
plotBsMA	plotBsMA
plotBsVolcano	plotBsVolcano
processingStepsFlowChart	processingStepsFlowChart
processingStepsTable	processingStepsTable
pureClipGeneWiseFilter	pureClipGeneWiseFilter
pureClipGlobalFilter	pureClipGlobalFilter
pureClipGlobalFilterPlot	pureClipGlobalFilterPlot
quickFigure	quickFigure
rangeCoveragePlot	rangeCoveragePlot
reproducibilityCutoffPlot	reproducibilityCutoffPlot
reproducibilityFilter	reproducibilityFilter
reproducibilityFilterPlot	reproducibilityFilterPlot
reproducibilitySamplesPlot	reproducibilitySamplesPlot
reproducibilityScatterPlot	reproducibilityScatterPlot
setMeta	setMeta
setMeta,BSFDataSet-method	setMeta
setName	setName
setName,BSFDataSet-method	setName
setRanges	setRanges
setRanges,BSFDataSet-method	setRanges
setSignal	setSignal
setSignal,BSFDataSet-method	setSignal
setSummary	setSummary
setSummary,BSFDataSet-method	setSummary
show	show
show,BSFDataSet-method	show
subset-BSFDataSet	subset-BSFDataSet
summary	summary
summary,BSFDataSet-method	summary
supportRatio	supportRatio
supportRatioPlot	supportRatioPlot
targetGeneSpectrumPlot	targetGeneSpectrumPlot
transcriptRegionOverlapsPlot	transcriptRegionOverlapsPlot
transcriptRegionSpectrumPlot	transcriptRegionSpectrumPlot
[,BSFDataSet,ANY,ANY,ANY-method	subset-BSFDataSet
