CAGEr-package	CAGEr-package
.byCtss	byCtss
.byCtss,data.table-method	byCtss
.ConsensusClusters	ConsensusClusters-class
.ctss_summary_for_clusters	dot-ctss_summary_for_clusters
.get.quant.pos	QuantileWidthFunctions
.hanabi	hanabi-class
.powerLaw	powerLaw
.TagClusters	TagClusters-class
aggregateTagClusters	aggregateTagClusters
aggregateTagClusters,CAGEr-method	aggregateTagClusters
annotateConsensusClusters	annotateCTSS
annotateConsensusClusters,CAGEexp,GRanges-method	annotateCTSS
annotateConsensusClusters,CAGEexp,TxDb-method	annotateCTSS
annotateCTSS	annotateCTSS
annotateCTSS,CAGEexp,GRanges-method	annotateCTSS
annotateCTSS,CAGEexp,TxDb-method	annotateCTSS
annotateTagClusters	annotateCTSS
annotateTagClusters,CAGEexp,GRanges-method	annotateCTSS
annotateTagClusters,CAGEexp,TxDb-method	annotateCTSS
bam2CTSS	bam2CTSS
CAGEexp	CAGEexp-class
CAGEexp-class	CAGEexp-class
CAGEr	CAGEr-package
CAGEr-class	CAGEr-class
CAGEr_Multicore	CAGEr_Multicore
coerce,CTSS,GRanges-method	CTSS-class
coerce,data.frame,CAGEexp-method	CAGEexp-class
coerce,GRanges,CTSS-method	CTSS-class
coerceInBSgenome	coerceInBSgenome
ConsensusClusters	ConsensusClusters-class
ConsensusClusters-class	ConsensusClusters-class
consensusClusters<-	consensusClusters-set
consensusClustersDESeq2	consensusClustersDESeq2
consensusClustersDESeq2,CAGEexp-method	consensusClustersDESeq2
consensusClustersGR	consensusClusters
consensusClustersGR,CAGEexp-method	consensusClusters
consensusClustersGR<-	consensusClusters-set
consensusClustersGR<-,CAGEexp-method	consensusClusters-set
consensusClustersQuantile	consensusClustersQuantile
consensusClustersQuantile,CAGEexp-method	consensusClustersQuantile
consensusClustersQuantileLow	consensusClustersQuantile
consensusClustersQuantileLow,CAGEexp-method	consensusClustersQuantile
consensusClustersQuantileLow<-	consensusClustersQuantile
consensusClustersQuantileUp	consensusClustersQuantile
consensusClustersQuantileUp,CAGEexp-method	consensusClustersQuantile
consensusClustersQuantileUp<-	consensusClustersQuantile
consensusClustersSE	consensusClusters
consensusClustersSE,CAGEexp-method	consensusClusters
consensusClustersSE<-	consensusClusters-set
consensusClustersSE<-,CAGEexp,RangedSummarizedExperiment-method	consensusClusters-set
consensusClustersTpm	consensusClustersTpm
consensusClustersTpm,CAGEexp-method	consensusClustersTpm
correlationMatrix	plotCorrelation
correlationMatrix,CAGEexp-method	plotCorrelation
correlationMatrix,data.frame-method	plotCorrelation
correlationMatrix,DataFrame-method	plotCorrelation
correlationMatrix,matrix-method	plotCorrelation
correlationMatrix,SummarizedExperiment-method	plotCorrelation
CTSS	CTSS-class
CTSS-class	CTSS-class
CTSScoordinatesGR	CTSScoordinates
CTSScoordinatesGR,CAGEexp-method	CTSScoordinates
CTSScoordinatesGR<-	CTSScoordinates
CTSScoordinatesGR<-,CAGEexp-method	CTSScoordinates
CTSScumulativesCC	CTSScumulativesTagClusters
CTSScumulativesCC,CAGEexp-method	CTSScumulativesTagClusters
CTSScumulativesTagClusters	CTSScumulativesTagClusters
CTSScumulativesTagClusters,CAGEexp-method	CTSScumulativesTagClusters
CTSScumulativesTagClusters<-	CTSScumulativesTagClusters
CTSScumulativesTagClusters<-,CAGEexp-method	CTSScumulativesTagClusters
CTSSnormalizedTpmDF	CTSSnormalizedTpm
CTSSnormalizedTpmDF,CAGEexp-method	CTSSnormalizedTpm
CTSSnormalizedTpmGR	CTSSnormalizedTpm
CTSSnormalizedTpmGR,CAGEexp-method	CTSSnormalizedTpm
CTSStagCountDF	CTSStagCount
CTSStagCountDF,CAGEexp-method	CTSStagCount
CTSStagCountGR	CTSStagCount
CTSStagCountGR,CAGEexp-method	CTSStagCount
CTSStagCountSE	CTSStagCount
CTSStagCountSE,CAGEexp-method	CTSStagCount
CTSStagCountSE<-	CTSScoordinates
CTSStagCountSE<-,CAGEexp-method	CTSScoordinates
CTSStoGenes	CTSStoGenes
CTSStoGenes,CAGEexp-method	CTSStoGenes
cumulativeCTSSdistribution	cumulativeCTSSdistribution
cumulativeCTSSdistribution,CAGEexp-method	cumulativeCTSSdistribution
CustomConsensusClusters	CustomConsensusClusters
CustomConsensusClusters,CAGEexp,GRanges-method	CustomConsensusClusters
distclu	distclu
distclu,CAGEexp-method	distclu
distclu,CTSS-method	distclu
distclu,SummarizedExperiment-method	distclu
exampleCAGEexp	exampleCAGEexp
exampleZv9_annot	exampleZv9_annot
exportToTrack	exportToTrack
exportToTrack,CAGEexp-method	exportToTrack
exportToTrack,ConsensusClusters-method	exportToTrack
exportToTrack,CTSS-method	exportToTrack
exportToTrack,GRanges-method	exportToTrack
exportToTrack,GRangesList-method	exportToTrack
exportToTrack,TagClusters-method	exportToTrack
expressionClasses	expressionClasses
expressionClasses,ConsensusClusters-method	expressionClasses
expressionClasses,CTSS-method	expressionClasses
FANTOM5humanSamples	FANTOM5humanSamples
FANTOM5mouseSamples	FANTOM5mouseSamples
filteredCTSSidx	filteredCTSSidx
filteredCTSSidx,CAGEexp-method	filteredCTSSidx
filterLowExpCTSS	flagLowExpCTSS
filterLowExpCTSS,CAGEr-method	flagLowExpCTSS
findStrandInvaders	strandInvaders
findStrandInvaders,CAGEexp-method	strandInvaders
findStrandInvaders,CTSS-method	strandInvaders
flagByUpstreamSequences	flagByUpstreamSequences
flagByUpstreamSequences,ConsensusClusters-method	flagByUpstreamSequences
flagByUpstreamSequences,CTSS-method	flagByUpstreamSequences
flagByUpstreamSequences,GRanges-method	flagByUpstreamSequences
flagByUpstreamSequences,TagClusters-method	flagByUpstreamSequences
flagLowExpCTSS	flagLowExpCTSS
flagLowExpCTSS,CAGEr-method	flagLowExpCTSS
flagLowExpCTSS,DataFrame-method	flagLowExpCTSS
flagLowExpCTSS,matrix-method	flagLowExpCTSS
flagLowExpCTSS,RangedSummarizedExperiment-method	flagLowExpCTSS
GeneExpDESeq2	GeneExpDESeq2
GeneExpDESeq2,CAGEexp-method	GeneExpDESeq2
GeneExpSE	GeneExpSE
GeneExpSE,CAGEexp-method	GeneExpSE
genomeName	genomeName
genomeName,CAGEexp-method	genomeName
genomeName,CTSS-method	genomeName
genomeName<-	genomeName
genomeName<-,CAGEexp-method	genomeName
genomeName<-,CTSS-method	genomeName
getCTSS	getCTSS
getCTSS,CAGEexp-method	getCTSS
getExpressionProfiles	getExpressionProfiles
getExpressionProfiles,CAGEexp-method	getExpressionProfiles
getExpressionProfiles,matrix-method	getExpressionProfiles
getShiftingPromoters	getShiftingPromoters
getShiftingPromoters,CAGEexp-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.bigwig	import.bigwig
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<-	inputFiles
inputFiles<-,CAGEexp-method	inputFiles
inputFilesType	inputFilesType
inputFilesType,CAGEexp-method	inputFilesType
inputFilesType<-	inputFilesType
inputFilesType<-,CAGEexp-method	inputFilesType
librarySizes	librarySizes
librarySizes,CAGEexp-method	librarySizes
lines.hanabi	plot.hanabi
loadFileIntoGPos	loadFileIntoGPos
mapStats	mapStats
mapStatsScopes	mapStatsScopes
mergeCAGEsets	mergeCAGEsets
mergeCAGEsets,CAGEexp,CAGEexp-method	mergeCAGEsets
mergeSamples	mergeSamples
mergeSamples,CAGEexp-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
paraclu	paraclu
paraclu,CAGEexp-method	paraclu
paraclu,CTSS-method	paraclu
paraclu,GRanges-method	paraclu
paraclu,Pairs-method	paraclu
paraclu,SummarizedExperiment-method	paraclu
parseCAGEscanBlocksToGrangeTSS	parseCAGEscanBlocksToGrangeTSS
plot.hanabi	plot.hanabi
plotAnnot	plotAnnot
plotAnnot,CAGEexp-method	plotAnnot
plotAnnot,data.frame-method	plotAnnot
plotAnnot,DataFrame-method	plotAnnot
plotAnnot,GRangesList-method	plotAnnot
plotCorrelation	plotCorrelation
plotCorrelation,CAGEr-method	plotCorrelation
plotCorrelation2	plotCorrelation
plotCorrelation2,CAGEexp-method	plotCorrelation
plotCorrelation2,data.frame-method	plotCorrelation
plotCorrelation2,DataFrame-method	plotCorrelation
plotCorrelation2,matrix-method	plotCorrelation
plotCorrelation2,SummarizedExperiment-method	plotCorrelation
plotExpressionProfiles	plotExpressionProfiles
plotExpressionProfiles,CAGEexp-method	plotExpressionProfiles
plotInterquantileWidth	plotInterquantileWidth
plotInterquantileWidth,CAGEexp-method	plotInterquantileWidth
plotReverseCumulatives	plotReverseCumulatives
plotReverseCumulatives,CAGEexp-method	plotReverseCumulatives
plotReverseCumulatives,GRanges-method	plotReverseCumulatives
plotReverseCumulatives,GRangesList-method	plotReverseCumulatives
points.hanabi	plot.hanabi
quantilePositions	quantilePositions
quantilePositions,CAGEexp-method	quantilePositions
quickEnhancers	quickEnhancers
quickEnhancers,CAGEexp-method	quickEnhancers
ranges2annot	ranges2annot
ranges2genes	ranges2genes
ranges2names	ranges2names
removeStrandInvaders	strandInvaders
removeStrandInvaders,CAGEexp-method	strandInvaders
removeStrandInvaders,CTSS-method	strandInvaders
resetCAGEexp	resetCAGEexp
resetCAGEexp,CAGEexp-method	resetCAGEexp
rowsum.RleDataFrame	rowsum.RleDataFrame
rowSums.RleDataFrame	rowSums.RleDataFrame
sampleLabels	sampleLabels
sampleLabels,CAGEexp-method	sampleLabels
sampleLabels,CTSS-method	sampleLabels
sampleLabels<-	sampleLabels
sampleLabels<-,CAGEexp-method	sampleLabels
sampleLabels<-,CTSS-method	sampleLabels
sampleList	sampleLabels
sampleList,CAGEr-method	sampleLabels
scoreShift	scoreShift
scoreShift,CAGEexp-method	scoreShift
seqNameTotalsSE	seqNameTotalsSE
seqNameTotalsSE,CAGEexp-method	seqNameTotalsSE
seqNameTotalsSE<-	seqNameTotalsSE
setColors	setColors
setColors,CAGEr-method	setColors
show,CTSS-method	CTSS-class
Strand invaders	strandInvaders
summariseChrExpr	summariseChrExpr
summariseChrExpr,CAGEexp-method	summariseChrExpr
TagClusters	TagClusters-class
TagClusters-class	TagClusters-class
tagClustersGR	tagClusters
tagClustersGR,CAGEexp-method	tagClusters
tagClustersGR<-	tagClusters
tagClustersGR<-,CAGEexp,ANY,TagClusters-method	tagClusters
tagClustersGR<-,CAGEexp,missing,GRangesList-method	tagClusters
TSSlogo	TSSlogo
TSSlogo,CAGEexp-method	TSSlogo
TSSlogo,ConsensusClusters-method	TSSlogo
TSSlogo,CTSS-method	TSSlogo
TSSlogo,TagClusters-method	TSSlogo
