AccessiblePeaks	AccessiblePeaks
AddChromatinModule	AddChromatinModule
AddMotifs	AddMotifs
AddMotifs.ChromatinAssay	AddMotifs
AddMotifs.default	AddMotifs
AddMotifs.Seurat	AddMotifs
AggregateTiles	AggregateTiles
AggregateTiles.ChromatinAssay	AggregateTiles
AggregateTiles.default	AggregateTiles
AggregateTiles.Seurat	AggregateTiles
AlleleFreq	AlleleFreq
AlleleFreq.Assay	AlleleFreq
AlleleFreq.default	AlleleFreq
AlleleFreq.Seurat	AlleleFreq
Annotation	Annotation
Annotation.ChromatinAssay	Annotation
Annotation.Seurat	Annotation
Annotation<-	Annotation
Annotation<-.ChromatinAssay	Annotation
Annotation<-.Seurat	Annotation
AnnotationPlot	AnnotationPlot
as.ChromatinAssay	as.ChromatinAssay
as.ChromatinAssay.Assay	as.ChromatinAssay
atac_small	atac_small
AverageCounts	AverageCounts
BigwigTrack	BigwigTrack
BinarizeCounts	BinarizeCounts
BinarizeCounts.Assay	BinarizeCounts
BinarizeCounts.default	BinarizeCounts
BinarizeCounts.Seurat	BinarizeCounts
blacklist_ce10	blacklist_ce10
blacklist_ce11	blacklist_ce11
blacklist_dm3	blacklist_dm3
blacklist_dm6	blacklist_dm6
blacklist_hg19	blacklist_hg19
blacklist_hg38	blacklist_hg38
blacklist_hg38_unified	blacklist_hg38_unified
blacklist_mm10	blacklist_mm10
CallPeaks	CallPeaks
CallPeaks.ChromatinAssay	CallPeaks
CallPeaks.default	CallPeaks
CallPeaks.Fragment	CallPeaks
CallPeaks.Seurat	CallPeaks
Cells	reexports
Cells.Fragment	Cells
Cells<-	Cells-set
Cells<-.Fragment	Cells
CellsPerGroup	CellsPerGroup
ChromatinAssay	ChromatinAssay-class
ChromatinAssay-class	ChromatinAssay-class
ClosestFeature	ClosestFeature
ClusterClonotypes	ClusterClonotypes
CombineTracks	CombineTracks
ConnectionsToLinks	ConnectionsToLinks
ConvertMotifID	ConvertMotifID
ConvertMotifID.ChromatinAssay	ConvertMotifID
ConvertMotifID.default	ConvertMotifID
ConvertMotifID.Motif	ConvertMotifID
ConvertMotifID.Seurat	ConvertMotifID
CountFragments	CountFragments
countOverlaps	findOverlaps-methods
countOverlaps,ChromatinAssay,ChromatinAssay-method	findOverlaps-methods
countOverlaps,ChromatinAssay,Vector-method	findOverlaps-methods
countOverlaps,Seurat,Seurat-method	findOverlaps-methods
countOverlaps,Seurat,Vector-method	findOverlaps-methods
countOverlaps,Vector,ChromatinAssay-method	findOverlaps-methods
countOverlaps,Vector,Seurat-method	findOverlaps-methods
CountsInRegion	CountsInRegion
coverage	coverage-ChromatinAssay-method
coverage,ChromatinAssay-method	coverage-ChromatinAssay-method
coverage,Seurat-method	coverage-ChromatinAssay-method
CoverageBrowser	CoverageBrowser
CoveragePlot	CoveragePlot
CreateChromatinAssay	CreateChromatinAssay
CreateFragmentObject	CreateFragmentObject
CreateMotifMatrix	CreateMotifMatrix
CreateMotifObject	CreateMotifObject
DepthCor	DepthCor
disjoin	inter-range-methods
disjoin,ChromatinAssay-method	inter-range-methods
disjoin,Seurat-method	inter-range-methods
disjointBins	inter-range-methods
disjointBins,ChromatinAssay-method	inter-range-methods
disjointBins,Seurat-method	inter-range-methods
distance	nearest-methods
distance,ANY,ChromatinAssay-method	nearest-methods
distance,ANY,Seurat-method	nearest-methods
distance,ChromatinAssay,ANY-method	nearest-methods
distance,ChromatinAssay,ChromatinAssay-method	nearest-methods
distance,Seurat,ANY-method	nearest-methods
distance,Seurat,Seurat-method	nearest-methods
distanceToNearest	nearest-methods
distanceToNearest,ANY,ChromatinAssay-method	nearest-methods
distanceToNearest,ANY,Seurat-method	nearest-methods
distanceToNearest,ChromatinAssay,ANY-method	nearest-methods
distanceToNearest,ChromatinAssay,ChromatinAssay-method	nearest-methods
distanceToNearest,Seurat,ANY-method	nearest-methods
distanceToNearest,Seurat,Seurat-method	nearest-methods
DownsampleFeatures	DownsampleFeatures
ExpressionPlot	ExpressionPlot
Extend	Extend
FeatureMatrix	FeatureMatrix
FilterCells	FilterCells
FindClonotypes	FindClonotypes
FindMotifs	FindMotifs
findOverlaps	findOverlaps-methods
findOverlaps,ChromatinAssay,ChromatinAssay-method	findOverlaps-methods
findOverlaps,ChromatinAssay,Vector-method	findOverlaps-methods
findOverlaps,Seurat,Seurat-method	findOverlaps-methods
findOverlaps,Seurat,Vector-method	findOverlaps-methods
findOverlaps,Vector,ChromatinAssay-method	findOverlaps-methods
findOverlaps,Vector,Seurat-method	findOverlaps-methods
findOverlaps-methods	findOverlaps-methods
FindTopFeatures	FindTopFeatures
FindTopFeatures.Assay	FindTopFeatures
FindTopFeatures.default	FindTopFeatures
FindTopFeatures.Seurat	FindTopFeatures
FoldChange	FoldChange
follow	nearest-methods
follow,ANY,ChromatinAssay-method	nearest-methods
follow,ANY,Seurat-method	nearest-methods
follow,ChromatinAssay,ANY-method	nearest-methods
follow,ChromatinAssay,ChromatinAssay-method	nearest-methods
follow,Seurat,ANY-method	nearest-methods
follow,Seurat,Seurat-method	nearest-methods
Footprint	Footprint
Footprint.ChromatinAssay	Footprint
Footprint.Seurat	Footprint
FractionCountsInRegion	FractionCountsInRegion
Fragment	Fragment-class
Fragment-class	Fragment-class
FragmentHistogram	FragmentHistogram
Fragments	Fragments
Fragments.ChromatinAssay	Fragments
Fragments.Seurat	Fragments
Fragments<-	Fragments
Fragments<-.ChromatinAssay	Fragments
Fragments<-.Seurat	Fragments
FRiP	FRiP
gaps	inter-range-methods
gaps,ChromatinAssay-method	inter-range-methods
gaps,Seurat-method	inter-range-methods
GeneActivity	GeneActivity
genome	seqinfo-methods
genome,ChromatinAssay-method	seqinfo-methods
genome,Seurat-method	seqinfo-methods
genome<-,ChromatinAssay-method	seqinfo-methods
genome<-,Seurat-method	seqinfo-methods
GenomeBinMatrix	GenomeBinMatrix
GetCellsInRegion	GetCellsInRegion
GetFootprintData	GetFootprintData
GetFragmentData	GetFragmentData
GetGRangesFromEnsDb	GetGRangesFromEnsDb
GetIntersectingFeatures	GetIntersectingFeatures
GetLinkedGenes	GetLinkedGenes
GetLinkedPeaks	GetLinkedPeaks
GetMotifData	GetMotifData
GetMotifData.ChromatinAssay	GetMotifData
GetMotifData.Motif	GetMotifData
GetMotifData.Seurat	GetMotifData
GetTSSPositions	GetTSSPositions
granges	granges-methods
granges,ChromatinAssay-method	granges-methods
granges,Seurat-method	granges-methods
granges-methods	granges-methods
GRangesToString	GRangesToString
head.Fragment	head.Fragment
IdentifyVariants	IdentifyVariants
IdentifyVariants.Assay	IdentifyVariants
IdentifyVariants.default	IdentifyVariants
IdentifyVariants.Seurat	IdentifyVariants
InsertionBias	InsertionBias
InsertionBias.ChromatinAssay	InsertionBias
InsertionBias.Seurat	InsertionBias
inter-range-methods	inter-range-methods
IntersectMatrix	IntersectMatrix
isCircular	seqinfo-methods
isCircular,ChromatinAssay-method	seqinfo-methods
isCircular,Seurat-method	seqinfo-methods
isCircular<-,ChromatinAssay-method	seqinfo-methods
isCircular<-,Seurat-method	seqinfo-methods
isDisjoint	inter-range-methods
isDisjoint,ChromatinAssay-method	inter-range-methods
isDisjoint,Seurat-method	inter-range-methods
Jaccard	Jaccard
LinkPeaks	LinkPeaks
LinkPlot	LinkPlot
Links	Links
Links.ChromatinAssay	Links
Links.Seurat	Links
Links<-	Links
Links<-.ChromatinAssay	Links
Links<-.Seurat	Links
LookupGeneCoords	LookupGeneCoords
MatchRegionStats	MatchRegionStats
Motif	Motif-class
Motif-class	Motif-class
MotifPlot	MotifPlot
Motifs	Motifs
Motifs.ChromatinAssay	Motifs
Motifs.Seurat	Motifs
Motifs<-	Motifs
Motifs<-.ChromatinAssay	Motifs
Motifs<-.Seurat	Motifs
nearest	nearest-methods
nearest,ANY,ChromatinAssay-method	nearest-methods
nearest,ANY,Seurat-method	nearest-methods
nearest,ChromatinAssay,ANY-method	nearest-methods
nearest,ChromatinAssay,ChromatinAssay-method	nearest-methods
nearest,Seurat,ANY-method	nearest-methods
nearest,Seurat,Seurat-method	nearest-methods
nearest-methods	nearest-methods
NucleosomeSignal	NucleosomeSignal
PeakPlot	PeakPlot
PlotFootprint	PlotFootprint
precede	nearest-methods
precede,ANY,ChromatinAssay-method	nearest-methods
precede,ANY,Seurat-method	nearest-methods
precede,ChromatinAssay,ANY-method	nearest-methods
precede,ChromatinAssay,ChromatinAssay-method	nearest-methods
precede,Seurat,ANY-method	nearest-methods
precede,Seurat,Seurat-method	nearest-methods
range	inter-range-methods
range,ChromatinAssay-method	inter-range-methods
range,Seurat-method	inter-range-methods
ReadMGATK	ReadMGATK
reduce	inter-range-methods
reduce,ChromatinAssay-method	inter-range-methods
reduce,Seurat-method	inter-range-methods
reexports	reexports
RegionStats	RegionStats
RegionStats.ChromatinAssay	RegionStats
RegionStats.default	RegionStats
RegionStats.Seurat	RegionStats
RunChromVAR	RunChromVAR
RunChromVAR.ChromatinAssay	RunChromVAR
RunChromVAR.Seurat	RunChromVAR
RunSVD	RunSVD
RunSVD.Assay	RunSVD
RunSVD.default	RunSVD
RunSVD.Seurat	RunSVD
RunTFIDF	RunTFIDF
RunTFIDF.Assay	RunTFIDF
RunTFIDF.default	RunTFIDF
RunTFIDF.Seurat	RunTFIDF
seqinfo	seqinfo-methods
seqinfo,ChromatinAssay-method	seqinfo-methods
seqinfo,Seurat-method	seqinfo-methods
seqinfo-methods	seqinfo-methods
seqinfo<-,ChromatinAssay-method	seqinfo-methods
seqinfo<-,Seurat-method	seqinfo-methods
seqlengths	seqinfo-methods
seqlengths,ChromatinAssay-method	seqinfo-methods
seqlengths,Seurat-method	seqinfo-methods
seqlengths<-,ChromatinAssay-method	seqinfo-methods
seqlengths<-,Seurat-method	seqinfo-methods
seqlevels	seqinfo-methods
seqlevels,ChromatinAssay-method	seqinfo-methods
seqlevels,Seurat-method	seqinfo-methods
seqlevels<-,ChromatinAssay-method	seqinfo-methods
seqlevels<-,Seurat-method	seqinfo-methods
seqnames	seqinfo-methods
seqnames,ChromatinAssay-method	seqinfo-methods
seqnames,Seurat-method	seqinfo-methods
seqnames<-,ChromatinAssay-method	seqinfo-methods
seqnames<-,Seurat-method	seqinfo-methods
SetMotifData	SetMotifData
SetMotifData.ChromatinAssay	SetMotifData
SetMotifData.Motif	SetMotifData
SetMotifData.Seurat	SetMotifData
SplitFragments	SplitFragments
StringToGRanges	StringToGRanges
subset	subset.Motif
subset.Motif	subset.Motif
SubsetMatrix	SubsetMatrix
theme_browser	theme_browser
TilePlot	TilePlot
TSSEnrichment	TSSEnrichment
TSSPlot	TSSPlot
UnifyPeaks	UnifyPeaks
UpdatePath	UpdatePath
ValidateCells	ValidateCells
ValidateFragments	ValidateFragments
ValidateHash	ValidateHash
VariantPlot	VariantPlot
[.Motif	subset.Motif
