All functions

AddMotifObject()

Add a Motif object to a Seurat object

AverageCounts()

AverageCounts

BinarizeCounts()

Binarize counts

CellsPerGroup()

CellsPerGroup

ClosestFeature()

ClosestFeature

CountsInRegion()

CountsInRegion

SingleCoveragePlot() CoveragePlot()

Plot Tn5 insertion sites over a region

CreateMotifMatrix()

CreateMotifMatrix

CreateMotifObject()

CreateMotifObject

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()

Find most frequently observed features

FractionCountsInRegion()

FractionCountsInRegion

FragmentHistogram()

Plot fragment length histogram

GRangesToString()

GRangesToString

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

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

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

StringToGRanges()

StringToGRanges

TSSEnrichment()

Compute TSS enrichment score per cell

TSSPlot()

Plot the enrichment around TSS

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