AddMotifObject	AddMotifObject
AddMotifObject.Assay	AddMotifObject
AddMotifObject.Seurat	AddMotifObject
atac_small	atac_small
AverageCounts	AverageCounts
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_mm10	blacklist_mm10
CellsPerGroup	CellsPerGroup
ClosestFeature	ClosestFeature
CountsInRegion	CountsInRegion
CoveragePlot	CoveragePlot
CreateMotifMatrix	CreateMotifMatrix
CreateMotifObject	CreateMotifObject
CutMatrix	CutMatrix
DepthCor	DepthCor
DownsampleFeatures	DownsampleFeatures
Extend	Extend
ExtractCell	ExtractCell
FeatureMatrix	FeatureMatrix
FilterFragments	FilterFragments
FindMotifs	FindMotifs
FindTopFeatures	FindTopFeatures
FindTopFeatures.Assay	FindTopFeatures
FindTopFeatures.default	FindTopFeatures
FindTopFeatures.Seurat	FindTopFeatures
FractionCountsInRegion	FractionCountsInRegion
FragmentHistogram	FragmentHistogram
FRiP	FRiP
GenomeBinMatrix	GenomeBinMatrix
GetCellsInRegion	GetCellsInRegion
GetFragments	GetFragments
GetIntersectingFeatures	GetIntersectingFeatures
GetMotifData	GetMotifData
GetMotifData.Assay	GetMotifData
GetMotifData.Motif	GetMotifData
GetMotifData.Seurat	GetMotifData
GetMotifObject	GetMotifObject
GetMotifObject.Assay	GetMotifObject
GetMotifObject.Seurat	GetMotifObject
GetReadsInRegion	GetReadsInRegion
GRangesToString	GRangesToString
IntersectMatrix	IntersectMatrix
Jaccard	Jaccard
MatchRegionStats	MatchRegionStats
MergeWithRegions	MergeWithRegions
Motif	Motif-class
Motif-class	Motif-class
MotifPlot	MotifPlot
NucleosomeSignal	NucleosomeSignal
RegionStats	RegionStats
RegionStats.Assay	RegionStats
RegionStats.default	RegionStats
RegionStats.Seurat	RegionStats
RunChromVAR	RunChromVAR
RunSVD	RunSVD
RunSVD.Assay	RunSVD
RunSVD.default	RunSVD
RunSVD.Seurat	RunSVD
RunTFIDF	RunTFIDF
RunTFIDF.Assay	RunTFIDF
RunTFIDF.default	RunTFIDF
RunTFIDF.Seurat	RunTFIDF
SetFragments	SetFragments
SetMotifData	SetMotifData
SetMotifData.Assay	SetMotifData
SetMotifData.Motif	SetMotifData
SetMotifData.Seurat	SetMotifData
SingleCoveragePlot	CoveragePlot
StringToGRanges	StringToGRanges
subset	subset.Motif
subset.Motif	subset.Motif
SubsetMatrix	SubsetMatrix
TSSEnrichment	TSSEnrichment
TSSPlot	TSSPlot
UnifyPeaks	UnifyPeaks
[.Motif	subset.Motif
