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
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
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
quantifyGenes	quantifyGenes
quickEnhancers	quickEnhancers
quickTSSs	quickTSSs
shapeEntropy	shapeEntropy
shapeIQR	shapeIQR
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
