ATACqc                  Compute scATAC-seq QC metrics
AccessiblePeaks         Accessible peaks
AddMotifs               Add DNA sequence motif information
AggregateTiles          Quantify aggregated genome tiles
AlleleFreq              Compute allele frequencies per cell
Annotation              Annotation
AnnotationPlot          Plot gene annotations
AverageCounts           Average Counts
BigwigTrack             Plot data from BigWig files
BinarizeCounts          Binarize counts
CallPeaks               Call peaks
Cells.Fragment          Set and get cell barcode information for a
                        'Fragment()' object
Cells<-                 Set and get cell barcode information for a
                        Fragment object
CellsPerGroup           Cells per group
ChromatinAssay-class    The ChromatinAssay class
ClosestFeature          Closest Feature
ClusterClonotypes       Find relationships between clonotypes
CombineTracks           Combine genome region plots
ConnectionsToLinks      Cicero connections to links
ConvertMotifID          Convert between motif name and motif ID
CountFragments          Count fragments
CountsInRegion          Counts in region
CoverageBrowser         Genome browser
CoveragePlot            Plot Tn5 insertion frequency over a region
CreateChromatinAssay    Create ChromatinAssay object
CreateFragmentObject    Create a Fragment object
CreateMotifMatrix       Create motif matrix
CreateMotifObject       Create motif object
DensityScatter          Scatterplot colored by point density
DepthCor                Plot sequencing depth correlation
DownsampleFeatures      Downsample Features
EnrichedTerms           Find enriched ontology terms
ExpressionPlot          Plot gene expression
Extend                  Extend
FRiP                    Calculate fraction of reads in peaks per cell
FeatureMatrix           Feature Matrix
FilterCells             Filter cells from fragment file
FindClonotypes          Find clonotypes
FindMotifs              FindMotifs
FindTopFeatures         Find most frequently observed features
FitMeanVar              Find variable features fitting LOESS
Footprint               Transcription factor footprinting analysis
FractionCountsInRegion
                        Fraction of counts in a genomic region
Fragment-class          The Fragment class
FragmentHistogram       Plot fragment length histogram
Fragments               Get the Fragment objects
GRangesToString         GRanges to String
GeneActivity            Create gene activity matrix
GenomeBinMatrix         Genome bin matrix
GetCellsInRegion        Get cells in a region
GetFootprintData        Get footprinting data
GetFragmentData         Get Fragment object data
GetGRangesFromEnsDb     Extract genomic ranges from EnsDb object
GetIntersectingFeatures
                        Find intersecting regions between two objects
GetLinkedGenes          Get genes linked to peaks
GetLinkedPeaks          Get peaks linked to genes
GetMotifData            Retrieve a motif matrix
GetTSSPositions         Find transcriptional start sites
IdentifyVariants        Identify mitochondrial variants
InsertionBias           Compute Tn5 insertion bias
IntersectMatrix         Intersect genomic coordinates with matrix rows
Jaccard                 Calculate the Jaccard index between two
                        matrices
LinkPeaks               Link peaks to genes
LinkPlot                Plot linked genomic elements
Links                   Get or set links information
LookupGeneCoords        Get gene coordinates
MatchRegionStats        Match DNA sequence characteristics
Motif-class             The Motif class
MotifCounts             Count fragments surrounding motif sites
MotifPlot               Plot DNA sequence motif
Motifs                  Get or set a motif information
NucleosomeSignal        NucleosomeSignal
PeakPlot                Plot peaks in a genomic region
PearsonResidualVar      Compute analytic Pearson residual variance
PlotFootprint           Plot motif footprinting results
ReadMGATK               Read MGATK output
RegionHeatmap           Region heatmap
RegionMatrix            Region enrichment analysis
RegionPlot              Region plot
RegionStats             Compute base composition information for
                        genomic ranges
RunSVD                  Run singular value decomposition
RunTFIDF                Compute the term-frequency
                        inverse-document-frequency
SetMotifData            Set motif data
SortIdents              Sorts cell metadata variable by similarity
                        using hierarchical clustering
SplitFragments          Split fragment file by cell identities
StringToGRanges         String to GRanges
SubsetMatrix            Subset matrix rows and columns
TSSEnrichment           Compute TSS enrichment score per cell
TSSPlot                 Plot signal enrichment around TSSs
TilePlot                Plot integration sites per cell
UnifyPeaks              Unify genomic ranges
UpdatePath              Update the file path for a Fragment object
ValidateCells           Validate cells present in fragment file
ValidateFragments       Validate Fragment object
ValidateHash            Validate hashes for Fragment object
VariantPlot             Plot strand concordance vs. VMR
as.ChromatinAssay       Convert objects to a ChromatinAssay
atac_small              A small example scATAC-seq dataset
blacklist_ce10          Genomic blacklist regions for C. elegans ce10
                        (0-based)
blacklist_ce11          Genomic blacklist regions for C. elegans ce11
                        (0-based)
blacklist_dm3           Genomic blacklist regions for Drosophila dm3
                        (0-based)
blacklist_dm6           Genomic blacklist regions for Drosophila dm6
                        (0-based)
blacklist_hg19          Genomic blacklist regions for Human hg19
                        (0-based)
blacklist_hg38          Genomic blacklist regions for Human GRCh38
blacklist_hg38_unified
                        Unified genomic blacklist regions for Human
                        GRCh38
blacklist_mm10          Genomic blacklist regions for Mouse mm10
                        (0-based)
coverage,ChromatinAssay-method
                        Coverage of a ChromatinAssay object
findOverlaps-methods    Find overlapping ranges for ChromatinAssay
                        objects
granges-methods         Access genomic ranges for ChromatinAssay
                        objects
head.Fragment           Return the first rows of a fragment file
inter-range-methods     Inter-range transformations for ChromatinAssay
                        objects
nearest-methods         Find the nearest range neighbors for
                        ChromatinAssay objects
seqinfo-methods         Access and modify sequence information for
                        ChromatinAssay objects
subset.Fragment         Subset a Fragment object
subset.Motif            Subset a Motif object
theme_browser           Genome browser theme
