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| AddMotifObject | Add a Motif object to a Seurat object |
| AddMotifObject.Assay | Add a Motif object to a Seurat object |
| AddMotifObject.Seurat | Add a Motif object to a Seurat object |
| atac_small | A small example scATAC-seq dataset |
| AverageCounts | Average Counts |
| BinarizeCounts | Binarize counts |
| BinarizeCounts.Assay | Binarize counts |
| BinarizeCounts.default | Binarize counts |
| BinarizeCounts.Seurat | Binarize counts |
| 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 |
| CellsPerGroup | Cells per group |
| ClosestFeature | Closest Feature |
| CountsInRegion | CountsInRegion |
| CoveragePlot | Plot Tn5 insertion sites over a region |
| CreateMotifMatrix | CreateMotifMatrix |
| CreateMotifObject | CreateMotifObject |
| CutMatrix | Generate matrix of integration sites |
| DepthCor | Sequencing depth correlation |
| DownsampleFeatures | DownsampleFeatures |
| Extend | Extend |
| ExtractCell | ExtractCell |
| FeatureMatrix | FeatureMatrix |
| FilterFragments | FilterFragments |
| FindMotifs | FindMotifs |
| FindTopFeatures | Find most frequently observed features |
| FindTopFeatures.Assay | Find most frequently observed features |
| FindTopFeatures.default | Find most frequently observed features |
| FindTopFeatures.Seurat | Find most frequently observed features |
| FractionCountsInRegion | FractionCountsInRegion |
| FragmentHistogram | Plot fragment length histogram |
| FRiP | Calculate fraction of reads in peaks per cell |
| GenomeBinMatrix | GenomeBinMatrix |
| GetCellsInRegion | GetCellsInRegion |
| GetFragments | GetFragments |
| GetIntersectingFeatures | Find interesecting regions between two objects |
| GetMotifData | Retrieve a motif matrix |
| GetMotifData.Assay | Retrieve a motif matrix |
| GetMotifData.Motif | Retrieve a motif matrix |
| GetMotifData.Seurat | Retrieve a motif matrix |
| GetMotifObject | Retrieve a Motif object |
| GetMotifObject.Assay | Retrieve a Motif object |
| GetMotifObject.Seurat | Retrieve a Motif object |
| GetReadsInRegion | GetReadsInRegion |
| GRangesToString | GRanges to String |
| 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 | The Motif class |
| Motif-class | The Motif class |
| MotifPlot | MotifPlot |
| NucleosomeSignal | NucleosomeSignal |
| RegionStats | Compute base composition information for genomic ranges |
| RegionStats.Assay | Compute base composition information for genomic ranges |
| RegionStats.default | Compute base composition information for genomic ranges |
| RegionStats.Seurat | Compute base composition information for genomic ranges |
| RunChromVAR | Run chromVAR |
| RunSVD | Run singular value decomposition |
| RunSVD.Assay | Run singular value decomposition |
| RunSVD.default | Run singular value decomposition |
| RunSVD.Seurat | Run singular value decomposition |
| RunTFIDF | Compute the term-frequency inverse-document-frequency |
| RunTFIDF.Assay | Compute the term-frequency inverse-document-frequency |
| RunTFIDF.default | Compute the term-frequency inverse-document-frequency |
| RunTFIDF.Seurat | Compute the term-frequency inverse-document-frequency |
| SetFragments | Set the fragments file path for creating plots |
| SetMotifData | Set motif data |
| SetMotifData.Assay | Set motif data |
| SetMotifData.Motif | Set motif data |
| SetMotifData.Seurat | Set motif data |
| SingleCoveragePlot | Plot Tn5 insertion sites over a region |
| StringToGRanges | String to GRanges |
| subset | Return a subset of a Motif object |
| subset.Motif | Return a subset of a Motif object |
| SubsetMatrix | Subset matrix rows and columns |
| TSSEnrichment | Compute TSS enrichment score per cell |
| TSSPlot | Plot the enrichment around TSS |
| UnifyPeaks | Unify genomic ranges |
| [.Motif | Return a subset of a Motif object |