AddMotifObject          Add a Motif object to a Seurat object
AverageCounts           Average Counts
BinarizeCounts          Binarize counts
CellsPerGroup           Cells per group
ClosestFeature          Closest Feature
CountsInRegion          CountsInRegion
CreateMotifMatrix       CreateMotifMatrix
CreateMotifObject       CreateMotifObject
CutMatrix               Generate matrix of integration sites
DepthCor                Sequencing depth correlation
DownsampleFeatures      DownsampleFeatures
Extend                  Extend
ExtractCell             ExtractCell
FRiP                    Calculate fraction of reads in peaks per cell
FeatureMatrix           FeatureMatrix
FilterFragments         FilterFragments
FindMotifs              FindMotifs
FindTopFeatures         Find most frequently observed features
FractionCountsInRegion
                        FractionCountsInRegion
FragmentHistogram       Plot fragment length histogram
GRangesToString         GRanges to String
GenomeBinMatrix         GenomeBinMatrix
GetCellsInRegion        GetCellsInRegion
GetFragments            GetFragments
GetIntersectingFeatures
                        Find interesecting regions between two objects
GetMotifData            Retrieve a motif matrix
GetMotifObject          Retrieve a Motif object
GetReadsInRegion        GetReadsInRegion
IntersectMatrix         Intersect genomic coordinates with matrix rows
Jaccard                 Calculate the Jaccard index between two
                        matrices
MatchRegionStats        Match DNA sequence characteristics
MergeWithRegions        Region-aware object merging
Motif-class             The Motif class
MotifPlot               MotifPlot
NucleosomeSignal        NucleosomeSignal
RegionStats             Compute base composition information for
                        genomic ranges
RunChromVAR             Run chromVAR
RunSVD                  Run singular value decomposition
RunTFIDF                Compute the term-frequency
                        inverse-document-frequency
SetFragments            Set the fragments file path for creating plots
SetMotifData            Set motif data
SingleCoveragePlot      Plot Tn5 insertion sites over a region
StringToGRanges         String to GRanges
SubsetMatrix            Subset matrix rows and columns
TSSEnrichment           Compute TSS enrichment score per cell
TSSPlot                 Plot the enrichment around TSS
UnifyPeaks              Unify genomic ranges
atac_small              A small example scATAC-seq dataset
blacklist_ce10          Genomic blacklist regions for C. elegans ce10
blacklist_ce11          Genomic blacklist regions for C. elegans ce11
blacklist_dm3           Genomic blacklist regions for Drosophila dm3
blacklist_dm6           Genomic blacklist regions for Drosophila dm6
blacklist_hg19          Genomic blacklist regions for Human hg19
blacklist_hg38          Genomic blacklist regions for Human GRCh38
blacklist_mm10          Genomic blacklist regions for Mouse mm10
subset.Motif            Return a subset of a Motif object
