CAGEr-package	CAGEr-package
.byCtss	byCtss
.byCtss,data.table-method	byCtss
.cluster.ctss.chr	distclu-functions
.cluster.ctss.strand	distclu-functions
.clusterAggregateAndSum	clusterAggregateAndSum
.clusterAggregateAndSum,data.frame-method	clusterAggregateAndSum
.clusterAggregateAndSum,data.table-method	clusterAggregateAndSum
.clusterAggregateAndSum,GRanges-method	clusterAggregateAndSum
.ctss2clusters	distclu-functions
.distclu	distclu-functions
.get.quant.pos	QuantileWidthFunctions
.getCAGEsignalCoverage	coverage-functions
.getCumsum	coverage-functions
.getCumsumChr2	coverage-functions
.hanabi	hanabi-class
.powerLaw	powerLaw
.summarize.clusters	distclu-functions
aggregateTagClusters	aggregateTagClusters
aggregateTagClusters,CAGEr-method	aggregateTagClusters
annotateConsensusClusters	annotateCTSS
annotateConsensusClusters,CAGEexp,GRanges-method	annotateCTSS
annotateConsensusClusters,CAGEset,ANY-method	annotateCTSS
annotateCTSS	annotateCTSS
annotateCTSS,CAGEexp,GRanges-method	annotateCTSS
annotateCTSS,CAGEset,ANY-method	annotateCTSS
bam2CTSS	bam2CTSS
CAGEexp	CAGEexp-class
CAGEexp-class	CAGEexp-class
CAGEr	CAGEr-class
CAGEr-class	CAGEr-class
CAGEr_Multicore	CAGEr_Multicore
CAGEset	CAGEset-class
CAGEset-class	CAGEset-class
CCdataframe2granges	consensusClusterConvertors
CCgranges2dataframe	consensusClusterConvertors
clusterCTSS	clusterCTSS
clusterCTSS,CAGEexp-method	clusterCTSS
clusterCTSS,CAGEset-method	clusterCTSS
coerce,CTSS,GRanges-method	CTSS-class
coerce,data.frame,CAGEexp-method	CAGEexp-class
coerce,data.frame,CAGEset-method	CAGEset-class
coerce,GRanges,CTSS-method	CTSS-class
coerceInBSgenome	coerceInBSgenome
consensusClusterConvertors	consensusClusterConvertors
consensusClusters	consensusClusters
consensusClusters,CAGEr-method	consensusClusters
consensusClusters<-	consensusClusters-set
consensusClusters<-,CAGEexp-method	consensusClusters-set
consensusClusters<-,CAGEset-method	consensusClusters-set
consensusClustersDESeq2	consensusClustersDESeq2
consensusClustersDESeq2,CAGEexp-method	consensusClustersDESeq2
consensusClustersDESeq2,CAGEset-method	consensusClustersDESeq2
consensusClustersGR	consensusClusters
consensusClustersGR,CAGEexp-method	consensusClusters
consensusClustersGR,CAGEset-method	consensusClusters
consensusClustersGR<-	consensusClusters-set
consensusClustersGR<-,CAGEexp-method	consensusClusters-set
consensusClustersGR<-,CAGEset-method	consensusClusters-set
consensusClustersQuantile	consensusClustersQuantile
consensusClustersQuantile,CAGEexp-method	consensusClustersQuantile
consensusClustersQuantile,CAGEset-method	consensusClustersQuantile
consensusClustersQuantileLow	consensusClustersQuantile
consensusClustersQuantileLow,CAGEexp-method	consensusClustersQuantile
consensusClustersQuantileLow,CAGEset-method	consensusClustersQuantile
consensusClustersQuantileLow<-	consensusClustersQuantile
consensusClustersQuantileLow<-,CAGEset-method	consensusClustersQuantile
consensusClustersQuantileUp	consensusClustersQuantile
consensusClustersQuantileUp,CAGEexp-method	consensusClustersQuantile
consensusClustersQuantileUp,CAGEset-method	consensusClustersQuantile
consensusClustersQuantileUp<-	consensusClustersQuantile
consensusClustersQuantileUp<-,CAGEset-method	consensusClustersQuantile
consensusClustersSE	consensusClusters
consensusClustersSE,CAGEexp-method	consensusClusters
consensusClustersSE,CAGEset-method	consensusClusters
consensusClustersSE<-	consensusClusters-set
consensusClustersSE<-,CAGEexp,RangedSummarizedExperiment-method	consensusClusters-set
consensusClustersSE<-,CAGEset,ANY-method	consensusClusters-set
consensusClustersTpm	consensusClustersTpm
consensusClustersTpm,CAGEexp-method	consensusClustersTpm
consensusClustersTpm,CAGEset-method	consensusClustersTpm
coverage-functions	coverage-functions
CTSS	CTSS-class
CTSS-class	CTSS-class
CTSS.chr-class	CTSS-class
CTSSclusteringMethod	CTSSclusteringMethod
CTSSclusteringMethod,CAGEexp-method	CTSSclusteringMethod
CTSSclusteringMethod,CAGEset-method	CTSSclusteringMethod
CTSSclusteringMethod,GRangesList-method	CTSSclusteringMethod
CTSSclusteringMethod<-	CTSSclusteringMethod
CTSSclusteringMethod<-,CAGEexp-method	CTSSclusteringMethod
CTSSclusteringMethod<-,CAGEset-method	CTSSclusteringMethod
CTSSclusteringMethod<-,GRangesList-method	CTSSclusteringMethod
CTSScoordinates	CTSScoordinates
CTSScoordinates,CAGEexp-method	CTSScoordinates
CTSScoordinates,CAGEset-method	CTSScoordinates
CTSScoordinatesGR	CTSScoordinates
CTSScoordinatesGR,CAGEexp-method	CTSScoordinates
CTSScoordinatesGR,CAGEset-method	CTSScoordinates
CTSScoordinatesGR<-	CTSScoordinates
CTSScoordinatesGR<-,CAGEexp-method	CTSScoordinates
CTSScoordinatesGR<-,CAGEset-method	CTSScoordinates
CTSScumulativesCC	CTSScumulativesTagClusters
CTSScumulativesCC,CAGEexp-method	CTSScumulativesTagClusters
CTSScumulativesCC,CAGEset-method	CTSScumulativesTagClusters
CTSScumulativesTagClusters	CTSScumulativesTagClusters
CTSScumulativesTagClusters,CAGEexp-method	CTSScumulativesTagClusters
CTSScumulativesTagClusters,CAGEset-method	CTSScumulativesTagClusters
CTSScumulativesTagClusters<-	CTSScumulativesTagClusters
CTSScumulativesTagClusters<-,CAGEexp-method	CTSScumulativesTagClusters
CTSScumulativesTagClusters<-,CAGEset-method	CTSScumulativesTagClusters
CTSSnormalizedTpm	CTSSnormalizedTpm
CTSSnormalizedTpm,CAGEexp-method	CTSSnormalizedTpm
CTSSnormalizedTpm,CAGEset-method	CTSSnormalizedTpm
CTSSnormalizedTpmDF	CTSSnormalizedTpm
CTSSnormalizedTpmDf	CTSSnormalizedTpm
CTSSnormalizedTpmDF,CAGEexp-method	CTSSnormalizedTpm
CTSSnormalizedTpmDf,CAGEexp-method	CTSSnormalizedTpm
CTSSnormalizedTpmDF,CAGEset-method	CTSSnormalizedTpm
CTSSnormalizedTpmDf,CAGEset-method	CTSSnormalizedTpm
CTSSnormalizedTpmGR	CTSSnormalizedTpm
CTSSnormalizedTpmGR,CAGEr-method	CTSSnormalizedTpm
CTSStagCount	CTSStagCount
CTSStagCount,CAGEexp-method	CTSStagCount
CTSStagCount,CAGEset-method	CTSStagCount
CTSStagCountDA	CTSStagCount
CTSStagCountDA,CAGEr-method	CTSStagCount
CTSStagCountDF	CTSStagCount
CTSStagCountDf	CTSStagCount
CTSStagCountDF,CAGEexp-method	CTSStagCount
CTSStagCountDf,CAGEexp-method	CTSStagCount
CTSStagCountDF,CAGEset-method	CTSStagCount
CTSStagCountDf,CAGEset-method	CTSStagCount
CTSStagCountGR	CTSStagCount
CTSStagCountGR,CAGEr-method	CTSStagCount
CTSStagCountSE	CTSStagCount
CTSStagCountSE,CAGEexp-method	CTSStagCountTable
CTSStagCountSE,CAGEset-method	CTSStagCountTable
CTSStagCountSE<-	CTSScoordinates
CTSStagCountSE<-,CAGEexp-method	CTSScoordinates
CTSStagCountSE<-,CAGEset-method	CTSScoordinates
CTSStagCountTable	CTSStagCountTable
CTSStagCountTable,CAGEexp-method	CTSStagCountTable
CTSStagCountTable,CAGEset-method	CTSStagCountTable
CTSStoGenes	CTSStoGenes
CTSStoGenes,CAGEexp-method	CTSStoGenes
CTSStoGenes,CAGEset-method	CTSStoGenes
cumulativeCTSSdistribution	cumulativeCTSSdistribution
cumulativeCTSSdistribution,CAGEr-method	cumulativeCTSSdistribution
CustomConsensusClusters	CustomConsensusClusters
CustomConsensusClusters,CAGEexp,GRanges-method	CustomConsensusClusters
distclu-functions	distclu-functions
exampleCAGEexp	exampleCAGEexp
exampleCAGEset	exampleCAGEset
exampleZv9_annot	exampleZv9_annot
exportCTSStoBedGraph	exportCTSStoBedGraph
exportCTSStoBedGraph,CAGEr-method	exportCTSStoBedGraph
exportToBed	exportToBed
exportToBed,CAGEr-method	exportToBed
expressionClasses	expressionClasses
expressionClasses,CAGEexp-method	expressionClasses
expressionClasses,CAGEset-method	expressionClasses
extractExpressionClass	extractExpressionClass
extractExpressionClass,CAGEexp-method	extractExpressionClass
extractExpressionClass,CAGEset-method	extractExpressionClass
FANTOM5humanSamples	FANTOM5humanSamples
FANTOM5mouseSamples	FANTOM5mouseSamples
findStrandInvaders	strandInvaders
findStrandInvaders,CAGEexp-method	strandInvaders
findStrandInvaders,CTSS-method	strandInvaders
GeneExpDESeq2	GeneExpDESeq2
GeneExpDESeq2,CAGEexp-method	GeneExpDESeq2
GeneExpDESeq2,CAGEset-method	GeneExpDESeq2
GeneExpSE	GeneExpSE
GeneExpSE,CAGEexp-method	GeneExpSE
GeneExpSE,CAGEset-method	GeneExpSE
genomeName	genomeName
genomeName,CAGEexp-method	genomeName
genomeName,CAGEset-method	genomeName
genomeName,CTSS-method	genomeName
genomeName<-	genomeName
genomeName<-,CAGEexp-method	genomeName
genomeName<-,CAGEset-method	genomeName
genomeName<-,CTSS-method	genomeName
getCTSS	getCTSS
getCTSS,CAGEexp-method	getCTSS
getCTSS,CAGEset-method	getCTSS
getExpressionProfiles	getExpressionProfiles
getExpressionProfiles,CAGEset-method	getExpressionProfiles
getShiftingPromoters	getShiftingPromoters
getShiftingPromoters,CAGEset-method	getShiftingPromoters
hanabi	hanabi
hanabi,GRanges-method	hanabi
hanabi,integer-method	hanabi
hanabi,List-method	hanabi
hanabi,list-method	hanabi
hanabi,matrix-method	hanabi
hanabi,numeric-method	hanabi
hanabi,Rle-method	hanabi
hanabi-class	hanabi-class
hanabiPlot	hanabiPlot
import.bam	import.bam
import.bam.ctss	import.bam.ctss
import.bedCTSS	import.bedCTSS
import.bedmolecule	import.bedmolecule
import.bedScore	import.bedScore
import.CAGEscanMolecule	import.CAGEscanMolecule
import.CTSS	import.CTSS
importPublicData	importPublicData
importPublicData,character,character,ANY,character-method	importPublicData
initialize,CTSS-method	CTSS-class
inputFiles	inputFiles
inputFiles,CAGEexp-method	inputFiles
inputFiles,CAGEset-method	inputFiles
inputFiles<-	inputFiles
inputFiles<-,CAGEexp-method	inputFiles
inputFiles<-,CAGEset-method	inputFiles
inputFilesType	inputFilesType
inputFilesType,CAGEexp-method	inputFilesType
inputFilesType,CAGEset-method	inputFilesType
inputFilesType<-	inputFilesType
inputFilesType<-,CAGEexp-method	inputFilesType
inputFilesType<-,CAGEset-method	inputFilesType
librarySizes	librarySizes
librarySizes,CAGEexp-method	librarySizes
librarySizes,CAGEset-method	librarySizes
lines.hanabi	plot.hanabi
loadFileIntoGPos	loadFileIntoGPos
mapStats	mapStats
mapStatsScopes	mapStatsScopes
mergeCAGEsets	mergeCAGEsets
mergeCAGEsets,CAGEexp,CAGEexp-method	mergeCAGEsets
mergeCAGEsets,CAGEset,CAGEset-method	mergeCAGEsets
mergeSamples	mergeSamples
mergeSamples,CAGEexp,ANY-method	mergeSamples
mergeSamples,CAGEset,numeric-method	mergeSamples
moleculesGR2CTSS	moleculesGR2CTSS
msScope_all	mapStatsScopes
msScope_annotation	mapStatsScopes
msScope_counts	mapStatsScopes
msScope_mapped	mapStatsScopes
msScope_qc	mapStatsScopes
msScope_steps	mapStatsScopes
normalizeTagCount	normalizeTagCount
normalizeTagCount,CAGEexp-method	normalizeTagCount
normalizeTagCount,CAGEset-method	normalizeTagCount
parseCAGEscanBlocksToGrangeTSS	parseCAGEscanBlocksToGrangeTSS
plot.hanabi	plot.hanabi
plotAnnot	plotAnnot
plotAnnot,CAGEexp-method	plotAnnot
plotAnnot,data.frame-method	plotAnnot
plotAnnot,DataFrame-method	plotAnnot
plotCorrelation	plotCorrelation
plotCorrelation,CAGEr-method	plotCorrelation
plotCorrelation2	plotCorrelation
plotCorrelation2,CAGEexp-method	plotCorrelation
plotCorrelation2,CAGEset-method	plotCorrelation
plotCorrelation2,data.frame-method	plotCorrelation
plotCorrelation2,DataFrame-method	plotCorrelation
plotCorrelation2,matrix-method	plotCorrelation
plotCorrelation2,SummarizedExperiment-method	plotCorrelation
plotExpressionProfiles	plotExpressionProfiles
plotExpressionProfiles,CAGEset-method	plotExpressionProfiles
plotInterquantileWidth	plotInterquantileWidth
plotInterquantileWidth,CAGEr-method	plotInterquantileWidth
plotReverseCumulatives	plotReverseCumulatives
plotReverseCumulatives,CAGEr-method	plotReverseCumulatives
points.hanabi	plot.hanabi
quantilePositions	quantilePositions
quantilePositions,CAGEr-method	quantilePositions
ranges2annot	ranges2annot
ranges2genes	ranges2genes
ranges2names	ranges2names
removeStrandInvaders	strandInvaders
removeStrandInvaders,CAGEexp-method	strandInvaders
removeStrandInvaders,CTSS-method	strandInvaders
sampleLabels	sampleLabels
sampleLabels,CAGEexp-method	sampleLabels
sampleLabels,CAGEset-method	sampleLabels
sampleLabels,CTSS-method	sampleLabels
sampleLabels<-	sampleLabels
sampleLabels<-,CAGEexp-method	sampleLabels
sampleLabels<-,CAGEset-method	sampleLabels
sampleLabels<-,CTSS-method	sampleLabels
sampleList	sampleLabels
sampleList,CAGEr-method	sampleLabels
scoreShift	scoreShift
scoreShift,CAGEset-method	scoreShift
seqNameTotalsSE	seqNameTotalsSE
seqNameTotalsSE,CAGEexp-method	seqNameTotalsSE
seqNameTotalsSE,CAGEset-method	seqNameTotalsSE
seqNameTotalsSE<-	seqNameTotalsSE
setColors	setColors
setColors,CAGEr-method	setColors
show,CAGEset-method	show-methods
show-methods	show-methods
Strand invaders	strandInvaders
summariseChrExpr	summariseChrExpr
summariseChrExpr,CAGEexp-method	summariseChrExpr
tagClusterConvertors	tagClusterConvertors
tagClusters	tagClusters
tagClusters,CAGEr-method	tagClusters
tagClustersGR	tagClusters
tagClustersGR,CAGEexp-method	tagClusters
tagClustersGR,CAGEset-method	tagClusters
tagClustersGR<-	tagClusters
tagClustersGR<-,CAGEexp,ANY,TagClusters-method	tagClusters
tagClustersGR<-,CAGEexp,missing,GRangesList-method	tagClusters
tagClustersGR<-,CAGEset,ANY,ANY-method	tagClusters
tagClustersQuantile	tagClustersQuantile
tagClustersQuantile,CAGEexp-method	tagClustersQuantile
tagClustersQuantile,TagClusters-method	tagClustersQuantile
tagClustersQuantileLow	tagClustersQuantile
tagClustersQuantileLow,CAGEexp-method	tagClustersQuantile
tagClustersQuantileLow,CAGEset-method	tagClustersQuantile
tagClustersQuantileLow<-	tagClustersQuantile
tagClustersQuantileLow<-,CAGEexp-method	tagClustersQuantile
tagClustersQuantileLow<-,CAGEset-method	tagClustersQuantile
tagClustersQuantileUp	tagClustersQuantile
tagClustersQuantileUp,CAGEexp-method	tagClustersQuantile
tagClustersQuantileUp,CAGEset-method	tagClustersQuantile
tagClustersQuantileUp<-	tagClustersQuantile
tagClustersQuantileUp<-,CAGEset-method	tagClustersQuantile
TCdataframe2granges	tagClusterConvertors
TCgranges2dataframe	tagClusterConvertors
