CAGEr-package	CAGEr-package
aggregateTagClusters	aggregateTagClusters
aggregateTagClusters,CAGEset-method	aggregateTagClusters
CAGEr	CAGEr-package
CAGEset	CAGEset-class
CAGEset-class	CAGEset-class
clusterCTSS	clusterCTSS
clusterCTSS,CAGEset-method	clusterCTSS
coerce,data.frame,CAGEset-method	CAGEset-class
consensusClusters	consensusClusters
consensusClusters,CAGEset-method	consensusClusters
consensusClustersTpm	consensusClustersTpm
consensusClustersTpm,CAGEset-method	consensusClustersTpm
CTSSclusteringMethod	CTSSclusteringMethod
CTSSclusteringMethod,CAGEset-method	CTSSclusteringMethod
CTSScoordinates	CTSScoordinates
CTSScoordinates,CAGEset-method	CTSScoordinates
CTSSnormalizedTpm	CTSSnormalizedTpm
CTSSnormalizedTpm,CAGEset-method	CTSSnormalizedTpm
CTSStagCount	CTSStagCount
CTSStagCount,CAGEset-method	CTSStagCount
cumulativeCTSSdistribution	cumulativeCTSSdistribution
cumulativeCTSSdistribution,CAGEset-method	cumulativeCTSSdistribution
exampleCAGEset	exampleCAGEset
exportCTSStoBedGraph	exportCTSStoBedGraph
exportCTSStoBedGraph,CAGEset-method	exportCTSStoBedGraph
exportToBed	exportToBed
exportToBed,CAGEset-method	exportToBed
expressionClasses	expressionClasses
expressionClasses,CAGEset-method	expressionClasses
extractExpressionClass	extractExpressionClass
extractExpressionClass,CAGEset-method	extractExpressionClass
FANTOM5humanSamples	FANTOM5humanSamples
FANTOM5mouseSamples	FANTOM5mouseSamples
genomeName	genomeName
genomeName,CAGEset-method	genomeName
getCTSS	getCTSS
getCTSS,CAGEset-method	getCTSS
getExpressionProfiles	getExpressionProfiles
getExpressionProfiles,CAGEset-method	getExpressionProfiles
getShiftingPromoters	getShiftingPromoters
getShiftingPromoters,CAGEset-method	getShiftingPromoters
importPublicData	importPublicData
importPublicData,character,character,ANY,character-method	importPublicData
inputFiles	inputFiles
inputFiles,CAGEset-method	inputFiles
inputFilesType	inputFilesType
inputFilesType,CAGEset-method	inputFilesType
librarySizes	librarySizes
librarySizes,CAGEset-method	librarySizes
mergeCAGEsets	mergeCAGEsets
mergeCAGEsets,CAGEset,CAGEset-method	mergeCAGEsets
mergeSamples	mergeSamples
mergeSamples,CAGEset,numeric-method	mergeSamples
normalizeTagCount	normalizeTagCount
normalizeTagCount,CAGEset-method	normalizeTagCount
plotCorrelation	plotCorrelation
plotCorrelation,CAGEset-method	plotCorrelation
plotExpressionProfiles	plotExpressionProfiles
plotExpressionProfiles,CAGEset-method	plotExpressionProfiles
plotInterquantileWidth	plotInterquantileWidth
plotInterquantileWidth,CAGEset-method	plotInterquantileWidth
plotReverseCumulatives	plotReverseCumulatives
plotReverseCumulatives,CAGEset-method	plotReverseCumulatives
quantilePositions	quantilePositions
quantilePositions,CAGEset-method	quantilePositions
sampleLabels	sampleLabels
sampleLabels,CAGEset-method	sampleLabels
scoreShift	scoreShift
scoreShift,CAGEset,character,character-method	scoreShift
setColors	setColors
setColors,CAGEset-method	setColors
show,CAGEset-method	show-methods
show-methods	show-methods
tagClusters	tagClusters
tagClusters,CAGEset-method	tagClusters
