ChIPpeakAnno-package	ChIPpeakAnno-package
$,bindist-method	bindist
$,permPool-method	permPool
$<-,bindist-method	bindist
$<-,permPool-method	permPool
addAncestors	addAncestors
addGeneIDs	addGeneIDs
addMetadata	addMetadata
annoGR	annoGR
annoGR,EnsDb-method	annoGR
annoGR,GRanges-method	annoGR
annoGR,TxDb-method	annoGR
annoGR-class	annoGR
annoPeaks	annoPeaks
annotatedPeak	annotatedPeak
annotatePeakInBatch	annotatePeakInBatch
assignChromosomeRegion	assignChromosomeRegion
bdp	bdp
bindist	bindist
bindist-class	bindist
bindist-method	bindist
binOverFeature	binOverFeature
binOverGene	binOverGene
binOverRegions	binOverRegions
ChIPpeakAnno	ChIPpeakAnno-package
ChIPpeakAnno-deprecated	ChIPpeakAnno-deprecated
cntOverlaps	cntOverlaps
coerce	annoGR
coerce,annoGR,GRanges-method	annoGR
coerce,GRanges,annoGR-method	annoGR
condenseMatrixByColnames	condenseMatrixByColnames
convert2EntrezID	convert2EntrezID
countPatternInSeqs	countPatternInSeqs
cumulativePercentage	cumulativePercentage
downstreams	downstreams
egOrgMap	egOrgMap
enrichedGO	enrichedGO
enrichmentPlot	enrichmentPlot
EnsDb2GR	EnsDb2GR
estFragmentLength	estFragmentLength
estLibSize	estLibSize
ExonPlusUtr.human.GRCh37	ExonPlusUtr.human.GRCh37
featureAlignedDistribution	featureAlignedDistribution
featureAlignedExtendSignal	featureAlignedExtendSignal
featureAlignedHeatmap	featureAlignedHeatmap
featureAlignedSignal	featureAlignedSignal
findEnhancers	findEnhancers
findMotifsInPromoterSeqs	findMotifsInPromoterSeqs
findOverlappingPeaks	findOverlappingPeaks
findOverlappingPeaks-deprecated	findOverlappingPeaks
findOverlapsOfPeaks	findOverlapsOfPeaks
genomicElementDistribution	genomicElementDistribution
genomicElementUpSetR	genomicElementUpSetR
getAllPeakSequence	getAllPeakSequence
getAnnotation	getAnnotation
getEnrichedGO	getEnrichedGO
getEnrichedPATH	getEnrichedPATH
getGeneSeq	getGeneSeq
getGO	getGO
getUniqueGOidCount	getUniqueGOidCount
getVennCounts	getVennCounts
HOT.spots	HOT.spots
hyperGtest	hyperGtest
IDRfilter	IDRfilter
info	annoGR
info,annoGR-method	annoGR
makeVennDiagram	makeVennDiagram
mergePlusMinusPeaks	mergePlusMinusPeaks
metagenePlot	metagenePlot
myPeakList	myPeakList
oligoFrequency	oligoFrequency
oligoSummary	oligoSummary
overlappingPeaks	findOverlapsOfPeaks
overlappingPeaks-class	findOverlapsOfPeaks
peakPermTest	peakPermTest
Peaks.Ste12.Replicate1	Peaks.Ste12.Replicate1
Peaks.Ste12.Replicate2	Peaks.Ste12.Replicate2
Peaks.Ste12.Replicate3	Peaks.Ste12.Replicate3
peaks1	peaks1
peaks2	peaks2
peaks3	peaks3
peaksNearBDP	peaksNearBDP
permPool	permPool
permPool-class	permPool
permPool-method	permPool
pie1	pie1
plotBinOverRegions	plotBinOverRegions
preparePool	preparePool
reCenterPeaks	reCenterPeaks
summarizeOverlapsByBins	summarizeOverlapsByBins
summarizePatternInPeaks	summarizePatternInPeaks
tileCount	tileCount
tileGRanges	tileGRanges
toGRanges	toGRanges
toGRanges,character-method	toGRanges
toGRanges,connection-method	toGRanges
toGRanges,data.frame-method	toGRanges
toGRanges,EnsDb-method	toGRanges
toGRanges,TxDb-method	toGRanges
translatePattern	translatePattern
TSS.human.GRCh37	TSS.human.GRCh37
TSS.human.GRCh38	TSS.human.GRCh38
TSS.human.NCBI36	TSS.human.NCBI36
TSS.mouse.GRCm38	TSS.mouse.GRCm38
TSS.mouse.NCBIM37	TSS.mouse.NCBIM37
TSS.rat.RGSC3.4	TSS.rat.RGSC3.4
TSS.rat.Rnor_5.0	TSS.rat.Rnor_5.0
TSS.zebrafish.Zv8	TSS.zebrafish.Zv8
TSS.zebrafish.Zv9	TSS.zebrafish.Zv9
TxDb2GR	TxDb2GR
wgEncodeTfbsV3	wgEncodeTfbsV3
write2FASTA	write2FASTA
xget	xget
