FractionCountsInRegion
Plot fragment length histogram
ExtractCell
Retrieve a Motif object
GetReadsInRegion
Calculate fraction of reads in peaks per cell
Intersect genomic coordinates with matrix rows
FeatureMatrix
FilterFragments
Calculate the Jaccard index between two matrices
DownsampleFeatures
Extend
Find interesecting regions between two objects
Genomic blacklist regions for C. elegans ce11
Region-aware object merging
Match DNA sequence characteristics
NucleosomeSignal
The Motif class
A small example scATAC-seq dataset
MotifPlot
Retrieve a motif matrix
Genomic blacklist regions for C. elegans ce10
CreateMotifMatrix
GRanges to String
GenomeBinMatrix
String to GRanges
Genomic blacklist regions for Human GRCh38
Compute base composition information for genomic ranges
Set motif data
Compute the term-frequency inverse-document-frequency
FindMotifs
Find most frequently observed features
Set the fragments file path for creating plots
Run singular value decomposition
GetFragments
GetCellsInRegion
Plot the enrichment around TSS
Unify genomic ranges
Run chromVAR
Genomic blacklist regions for Drosophila dm3
Subset matrix rows and columns
Genomic blacklist regions for Mouse mm10
Genomic blacklist regions for Drosophila dm6
Genomic blacklist regions for Human hg19
Compute TSS enrichment score per cell
Return a subset of a Motif object
Add a Motif object to a Seurat object
Generate matrix of integration sites
CountsInRegion
Cells per group
Closest Feature
Plot Tn5 insertion sites over a region
Binarize counts
CreateMotifObject
Average Counts