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