assignGeneID	assignGeneID
assignGeneID,GenomicRanges,GenomicRanges-method	assignGeneID
assignGeneID,GenomicRanges,TxDb-method	assignGeneID
assignGeneID,RangedSummarizedExperiment,GenomicRanges-method	assignGeneID
assignGeneID,RangedSummarizedExperiment,TxDb-method	assignGeneID
assignMissingID	assignMissingID
assignMissingID,character-method	assignMissingID
assignMissingID,GenomicRanges-method	assignMissingID
assignMissingID,RangedSummarizedExperiment-method	assignMissingID
assignTxID	assignTxID
assignTxID,GenomicRanges,GenomicRanges-method	assignTxID
assignTxID,GenomicRanges,TxDb-method	assignTxID
assignTxID,RangedSummarizedExperiment,GenomicRanges-method	assignTxID
assignTxID,RangedSummarizedExperiment,TxDb-method	assignTxID
assignTxType	assignTxType
assignTxType,GenomicRanges,GenomicRangesList-method	assignTxType
assignTxType,GenomicRanges,TxDb-method	assignTxType
assignTxType,RangedSummarizedExperiment,GenomicRangesList-method	assignTxType
assignTxType,RangedSummarizedExperiment,TxDb-method	assignTxType
balanceBC	balanceBC
balanceD	balanceD
bwCommonGenome	bwCommonGenome
bwGenomeCompatibility	bwGenomeCompatibility
bwValid	bwValid
bwValid,BigWigFile-method	bwValid
bwValid,BigWigFileList-method	bwValid
calcBidirectionality	calcBidirectionality
calcBidirectionality,GPos-method	calcBidirectionality
calcBidirectionality,GRanges-method	calcBidirectionality
calcBidirectionality,RangedSummarizedExperiment-method	calcBidirectionality
calcComposition	calcComposition
calcPooled	calcPooled
calcShape	calcShape
calcShape,GRanges,GPos-method	calcShape
calcShape,GRanges,GRanges-method	calcShape
calcShape,GRanges,RangedSummarizedExperiment-method	calcShape
calcShape,RangedSummarizedExperiment,GRanges-method	calcShape
calcShape,RangedSummarizedExperiment,RangedSummarizedExperiment-method	calcShape
calcSupport	calcSupport
calcTotalTags	calcTotalTags
calcTPM	calcTPM
checkCTSSs	checkCTSSs
checkCTSSs,ANY-method	checkCTSSs
checkCTSSs,BigWigFile-method	checkCTSSs
checkCTSSs,character-method	checkCTSSs
checkCTSSs,GPos-method	checkCTSSs
checkCTSSs,GRanges-method	checkCTSSs
checkPeaked	checkPeaked
checkPooled	checkPooled
clusterBidirectionally	clusterBidirectionally
clusterBidirectionally,GPos-method	clusterBidirectionally
clusterBidirectionally,GRanges-method	clusterBidirectionally
clusterBidirectionally,RangedSummarizedExperiment-method	clusterBidirectionally
clusterUnidirectionally	clusterUnidirectionally
clusterUnidirectionally,GPos-method	clusterUnidirectionally
clusterUnidirectionally,GRanges-method	clusterUnidirectionally
clusterUnidirectionally,RangedSummarizedExperiment-method	clusterUnidirectionally
combineClusters	combineClusters
combineClusters,RangedSummarizedExperiment,RangedSummarizedExperiment-method	combineClusters
convertBAM2BigWig	convertBAM2BigWig
convertBED2BedGraph	convertBED2BigWig
convertBED2BigWig	convertBED2BigWig
convertBedGraph2BED	convertBED2BigWig
convertBedGraph2BigWig	convertBED2BigWig
convertBigWig2BED	convertBED2BigWig
convertBigWig2BedGraph	convertBED2BigWig
convertGRanges2GPos	convertGRanges2GPos
exampleBidirectional	exampleDesign
exampleCTSSs	exampleDesign
exampleDesign	exampleDesign
exampleGenes	exampleDesign
exampleUnidirectional	exampleDesign
findLinks	findLinks
findLinks,GRanges-method	findLinks
findLinks,RangedSummarizedExperiment-method	findLinks
findStretches	findStretches
findStretches,GRanges-method	findStretches
findStretches,RangedSummarizedExperiment-method	findStretches
quantifyClusters	quantifyClusters
quantifyCTSSs	quantifyCTSSs
quantifyCTSSs,BigWigFileList,BigWigFileList-method	quantifyCTSSs
quantifyCTSSs,character,character-method	quantifyCTSSs
quantifyCTSSs2	quantifyCTSSs2
quantifyGenes	quantifyGenes
quickEnhancers	quickEnhancers
quickGenes	quickGenes
quickTSSs	quickTSSs
shapeEntropy	shapeEntropy
shapeIQR	shapeIQR
shapeMean	shapeMean
shapeMultimodality	shapeMultimodality
subsetByBidirectionality	subsetByBidirectionality
subsetByBidirectionality,GPos-method	subsetByBidirectionality
subsetByBidirectionality,GRanges-method	subsetByBidirectionality
subsetByBidirectionality,RangedSummarizedExperiment-method	subsetByBidirectionality
subsetByComposition	subsetByComposition
subsetBySupport	subsetBySupport
swapRanges	swapRanges
swapRanges,GenomicRanges-method	swapRanges
swapRanges,RangedSummarizedExperiment-method	swapRanges
swapScores	swapScores
trackBalance	trackBalance
trackBalance,GPos-method	trackBalance
trackBalance,GRanges-method	trackBalance
trackBalance,RangedSummarizedExperiment-method	trackBalance
trackClusters	trackClusters
trackClusters,GRanges-method	trackClusters
trackClusters,RangedSummarizedExperiment-method	trackClusters
trackCTSS	trackCTSS
trackCTSS,GPos-method	trackCTSS
trackCTSS,GRanges-method	trackCTSS
trackCTSS,RangedSummarizedExperiment-method	trackCTSS
trackLinks	trackLinks
trimToPeak	trimToPeak
trimToPeak,GRanges,GPos-method	trimToPeak
trimToPeak,GRanges,GRanges-method	trimToPeak
trimToPeak,GRanges,RangedSummarizedExperiment-method	trimToPeak
trimToPeak,RangedSummarizedExperiment,GenomicRanges-method	trimToPeak
trimToPeak,RangedSummarizedExperiment,RangedSummarizedExperiment-method	trimToPeak
trimToPercentiles	trimToPercentiles
trimToPercentiles,GRanges,GPos-method	trimToPercentiles
trimToPercentiles,GRanges,GRanges-method	trimToPercentiles
trimToPercentiles,GRanges,RangedSummarizedExperiment-method	trimToPercentiles
trimToPercentiles,RangedSummarizedExperiment,GenomicRanges-method	trimToPercentiles
trimToPercentiles,RangedSummarizedExperiment,RangedSummarizedExperiment-method	trimToPercentiles
tuneTagClustering	tuneTagClustering
tuneTagClustering,GPos-method	tuneTagClustering
tuneTagClustering,GRanges-method	tuneTagClustering
tuneTagClustering,RangedSummarizedExperiment-method	tuneTagClustering
utilsAggregateRows	utilsAggregateRows
utilsAggregateRows,dgCMatrix-method	utilsAggregateRows
utilsAggregateRows,matrix-method	utilsAggregateRows
utilsDeStrand	utilsDeStrand
utilsScoreOverlaps	utilsScoreOverlaps
utilsSimplifyTxDb	utilsSimplifyTxDb
