All functions

AddMotifObject()

AddMotifObject

ApplyMatrixByGroup()

Apply function to integration sites per base per group

AverageCounts()

AverageCounts

BinarizeCounts()

BinarizeCounts

CellsPerGroup()

CellsPerGroup

ChunkGRanges()

ChunkGRanges

ClosestFeature()

ClosestFeature

ClusterMotifs()

ClusterMotifs

CountsInRegion()

CountsInRegion

SingleCoveragePlot() CoveragePlot()

CoveragePlot

CreateMotifMatrix()

CreateMotifMatrix

CreateMotifObject()

CreateMotifObject

CreateRegionPileupMatrix()

Create cut site pileup matrix

CutMatrix()

Generate matrix of integration sites

DownsampleFeatures()

DownsampleFeatures

Extend()

Extend

ExtractCell()

ExtractCell

FRiP()

Calculate fraction of reads in peaks per cell

FeatureMatrix()

FeatureMatrix

FilterFragments()

FilterFragments

FindMotifs()

FindMotifs

FindTopFeatures()

FindTopFeatures

FractionCountsInRegion()

FractionCountsInRegion

GRangesToString()

GRangesToString

GenomeBinMatrix()

GenomeBinMatrix

GetCellsInRegion()

GetCellsInRegion

GetFragments()

GetFragments

GetGroups()

Get vector of cell names and associated identity

GetIntersectingFeatures()

Find interesecting regions between two objects

GetMotifData()

GetMotifData

GetMotifObject()

GetMotifObject

GetReadsInRegion()

GetReadsInRegion

InsertionBias()

Compute Tn5 insertion bias

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

MotifDimPlot()

MotifDimPlot

MotifPlot()

MotifPlot

MultiRegionCutMatrix()

Generate cut matrix for many regions

NucleosomeSignal()

NucleosomeSignal

PeriodPlot()

Plot fragment length periodicity

RegionPileup()

Plot pileup of Tn5 integration sites

RegionStats()

Compute base composition information for genomic ranges

RunChromVAR()

Run chromVAR

RunMotifTSNE()

RunMotifTSNE

RunMotifUMAP()

RunMotifUMAP

RunSVD()

RunSVD

RunTFIDF()

RunTFIDF

SetFragments()

Set the fragments file path for creating plots

SetMotifData()

SetMotifData

StringToGRanges()

StringToGRanges

TSSEnrichment()

Compute TSS enrichment score per cell

TSSPlot()

Plot the enrichment around TSS

TabixOutputToDataFrame()

TabixOutputToDataFrame

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>) `[`(<Motif>)

Return a subset of a Motif object