Analysis of Single-Cell Chromatin Data
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Documentation for package ‘Signac’ version 1.13.0
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A B C D E F G H I J L M N P R S T U V misc
| Signac-package | Signac: Analysis of Single-Cell Chromatin Data |
-- A --
| AccessiblePeaks | Accessible peaks |
| AddChromatinModule | Add chromatin module |
| AddMotifs | Add DNA sequence motif information |
| AddMotifs.Assay | Add DNA sequence motif information |
| AddMotifs.ChromatinAssay | Add DNA sequence motif information |
| AddMotifs.default | Add DNA sequence motif information |
| AddMotifs.Seurat | Add DNA sequence motif information |
| AddMotifs.StdAssay | Add DNA sequence motif information |
| AggregateTiles | Quantify aggregated genome tiles |
| AggregateTiles.ChromatinAssay | Quantify aggregated genome tiles |
| AggregateTiles.default | Quantify aggregated genome tiles |
| AggregateTiles.Seurat | Quantify aggregated genome tiles |
| AlleleFreq | Compute allele frequencies per cell |
| AlleleFreq.Assay | Compute allele frequencies per cell |
| AlleleFreq.default | Compute allele frequencies per cell |
| AlleleFreq.Seurat | Compute allele frequencies per cell |
| AlleleFreq.StdAssay | Compute allele frequencies per cell |
| Annotation | Annotation |
| Annotation.ChromatinAssay | Annotation |
| Annotation.Seurat | Annotation |
| Annotation<- | Annotation |
| Annotation<-.ChromatinAssay | Annotation |
| Annotation<-.Seurat | Annotation |
| AnnotationPlot | Plot gene annotations |
| as.ChromatinAssay | Convert objects to a ChromatinAssay |
| as.ChromatinAssay.Assay | Convert objects to a ChromatinAssay |
| atac_small | A small example scATAC-seq dataset |
| AverageCounts | Average Counts |
-- B --
| BigwigTrack | Plot data from BigWig files |
| BinarizeCounts | Binarize counts |
| BinarizeCounts.Assay | Binarize counts |
| BinarizeCounts.default | Binarize counts |
| BinarizeCounts.Seurat | Binarize counts |
| blacklist_ce10 | Genomic blacklist regions for C. elegans ce10 (0-based) |
| blacklist_ce11 | Genomic blacklist regions for C. elegans ce11 (0-based) |
| blacklist_dm3 | Genomic blacklist regions for Drosophila dm3 (0-based) |
| blacklist_dm6 | Genomic blacklist regions for Drosophila dm6 (0-based) |
| blacklist_hg19 | Genomic blacklist regions for Human hg19 (0-based) |
| blacklist_hg38 | Genomic blacklist regions for Human GRCh38 |
| blacklist_hg38_unified | Unified genomic blacklist regions for Human GRCh38 |
| blacklist_mm10 | Genomic blacklist regions for Mouse mm10 (0-based) |
-- C --
| CallPeaks | Call peaks |
| CallPeaks.ChromatinAssay | Call peaks |
| CallPeaks.default | Call peaks |
| CallPeaks.Fragment | Call peaks |
| CallPeaks.Seurat | Call peaks |
| Cells.Fragment | Set and get cell barcode information for a 'Fragment' object |
| Cells<- | Set and get cell barcode information for a Fragment object |
| Cells<-.Fragment | Set and get cell barcode information for a 'Fragment' object |
| CellsPerGroup | Cells per group |
| ChromatinAssay | The ChromatinAssay class |
| ChromatinAssay-class | The ChromatinAssay class |
| ClosestFeature | Closest Feature |
| ClusterClonotypes | Find relationships between clonotypes |
| CombineTracks | Combine genome region plots |
| ConnectionsToLinks | Cicero connections to links |
| ConvertMotifID | Convert between motif name and motif ID |
| ConvertMotifID.Assay | Convert between motif name and motif ID |
| ConvertMotifID.ChromatinAssay | Convert between motif name and motif ID |
| ConvertMotifID.default | Convert between motif name and motif ID |
| ConvertMotifID.Motif | Convert between motif name and motif ID |
| ConvertMotifID.Seurat | Convert between motif name and motif ID |
| ConvertMotifID.StdAssay | Convert between motif name and motif ID |
| CountFragments | Count fragments |
| countOverlaps | Find overlapping ranges for ChromatinAssay objects |
| countOverlaps-method | Find overlapping ranges for ChromatinAssay objects |
| CountsInRegion | Counts in region |
| coverage | Coverage of a ChromatinAssay object |
| coverage-method | Coverage of a ChromatinAssay object |
| CoverageBrowser | Genome browser |
| CoveragePlot | Plot Tn5 insertion frequency over a region |
| CreateChromatinAssay | Create ChromatinAssay object |
| CreateFragmentObject | Create a Fragment object |
| CreateMotifMatrix | Create motif matrix |
| CreateMotifObject | Create motif object |
-- D --
| DensityScatter | Scatterplot colored by point density |
| DepthCor | Plot sequencing depth correlation |
| disjoin | Inter-range transformations for ChromatinAssay objects |
| disjoin-method | Inter-range transformations for ChromatinAssay objects |
| disjointBins | Inter-range transformations for ChromatinAssay objects |
| disjointBins-method | Inter-range transformations for ChromatinAssay objects |
| distance | Find the nearest range neighbors for ChromatinAssay objects |
| distance-method | Find the nearest range neighbors for ChromatinAssay objects |
| distanceToNearest | Find the nearest range neighbors for ChromatinAssay objects |
| distanceToNearest-method | Find the nearest range neighbors for ChromatinAssay objects |
| DownsampleFeatures | Downsample Features |
-- E --
| ExpressionPlot | Plot gene expression |
| Extend | Extend |
-- F --
| FeatureMatrix | Feature Matrix |
| FilterCells | Filter cells from fragment file |
| FindClonotypes | Find clonotypes |
| FindMotifs | FindMotifs |
| findOverlaps | Find overlapping ranges for ChromatinAssay objects |
| findOverlaps-method | Find overlapping ranges for ChromatinAssay objects |
| findOverlaps-methods | Find overlapping ranges for ChromatinAssay objects |
| 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 |
| FindTopFeatures.StdAssay | Find most frequently observed features |
| follow | Find the nearest range neighbors for ChromatinAssay objects |
| follow-method | Find the nearest range neighbors for ChromatinAssay objects |
| Footprint | Transcription factor footprinting analysis |
| Footprint.ChromatinAssay | Transcription factor footprinting analysis |
| Footprint.Seurat | Transcription factor footprinting analysis |
| FractionCountsInRegion | Fraction of counts in a genomic region |
| Fragment | The Fragment class |
| Fragment-class | The Fragment class |
| FragmentHistogram | Plot fragment length histogram |
| Fragments | Get the Fragment objects |
| Fragments.ChromatinAssay | Get the Fragment objects |
| Fragments.Seurat | Get the Fragment objects |
| Fragments<- | Get the Fragment objects |
| Fragments<-.ChromatinAssay | Get the Fragment objects |
| Fragments<-.Seurat | Get the Fragment objects |
| FRiP | Calculate fraction of reads in peaks per cell |
-- G --
| gaps | Inter-range transformations for ChromatinAssay objects |
| gaps-method | Inter-range transformations for ChromatinAssay objects |
| GeneActivity | Create gene activity matrix |
| genome | Access and modify sequence information for ChromatinAssay objects |
| genome-method | Access and modify sequence information for ChromatinAssay objects |
| genome<--method | Access and modify sequence information for ChromatinAssay objects |
| GenomeBinMatrix | Genome bin matrix |
| GetCellsInRegion | Get cells in a region |
| GetFootprintData | Get footprinting data |
| GetFragmentData | Get Fragment object data |
| GetGRangesFromEnsDb | Extract genomic ranges from EnsDb object |
| GetIntersectingFeatures | Find intersecting regions between two objects |
| GetLinkedGenes | Get genes linked to peaks |
| GetLinkedPeaks | Get peaks linked to genes |
| GetMotifData | Retrieve a motif matrix |
| GetMotifData.ChromatinAssay | Retrieve a motif matrix |
| GetMotifData.Motif | Retrieve a motif matrix |
| GetMotifData.Seurat | Retrieve a motif matrix |
| GetTSSPositions | Find transcriptional start sites |
| granges | Access genomic ranges for ChromatinAssay objects |
| granges-method | Access genomic ranges for ChromatinAssay objects |
| granges-methods | Access genomic ranges for ChromatinAssay objects |
| GRangesToString | GRanges to String |
-- H --
| head.Fragment | Return the first rows of a fragment file |
-- I --
| IdentifyVariants | Identify mitochondrial variants |
| IdentifyVariants.Assay | Identify mitochondrial variants |
| IdentifyVariants.default | Identify mitochondrial variants |
| IdentifyVariants.Seurat | Identify mitochondrial variants |
| IdentifyVariants.StdAssay | Identify mitochondrial variants |
| InsertionBias | Compute Tn5 insertion bias |
| InsertionBias.ChromatinAssay | Compute Tn5 insertion bias |
| InsertionBias.Seurat | Compute Tn5 insertion bias |
| inter-range-methods | Inter-range transformations for ChromatinAssay objects |
| IntersectMatrix | Intersect genomic coordinates with matrix rows |
| isCircular | Access and modify sequence information for ChromatinAssay objects |
| isCircular-method | Access and modify sequence information for ChromatinAssay objects |
| isCircular<--method | Access and modify sequence information for ChromatinAssay objects |
| isDisjoint | Inter-range transformations for ChromatinAssay objects |
| isDisjoint-method | Inter-range transformations for ChromatinAssay objects |
-- J --
| Jaccard | Calculate the Jaccard index between two matrices |
-- L --
| LinkPeaks | Link peaks to genes |
| LinkPlot | Plot linked genomic elements |
| Links | Get or set links information |
| Links.ChromatinAssay | Get or set links information |
| Links.Seurat | Get or set links information |
| Links<- | Get or set links information |
| Links<-.ChromatinAssay | Get or set links information |
| Links<-.Seurat | Get or set links information |
| LookupGeneCoords | Get gene coordinates |
-- M --
| MatchRegionStats | Match DNA sequence characteristics |
| Motif | The Motif class |
| Motif-class | The Motif class |
| MotifCounts | Count fragments surrounding motif sites |
| MotifPlot | Plot DNA sequence motif |
| Motifs | Get or set a motif information |
| Motifs.ChromatinAssay | Get or set a motif information |
| Motifs.Seurat | Get or set a motif information |
| Motifs<- | Get or set a motif information |
| Motifs<-.ChromatinAssay | Get or set a motif information |
| Motifs<-.Seurat | Get or set a motif information |
-- N --
| nearest | Find the nearest range neighbors for ChromatinAssay objects |
| nearest-method | Find the nearest range neighbors for ChromatinAssay objects |
| nearest-methods | Find the nearest range neighbors for ChromatinAssay objects |
| NucleosomeSignal | NucleosomeSignal |
-- P --
| PeakPlot | Plot peaks in a genomic region |
| PlotFootprint | Plot motif footprinting results |
| precede | Find the nearest range neighbors for ChromatinAssay objects |
| precede-method | Find the nearest range neighbors for ChromatinAssay objects |
-- R --
| range | Inter-range transformations for ChromatinAssay objects |
| range-method | Inter-range transformations for ChromatinAssay objects |
| ReadMGATK | Read MGATK output |
| reduce | Inter-range transformations for ChromatinAssay objects |
| reduce-method | Inter-range transformations for ChromatinAssay objects |
| RegionHeatmap | Region heatmap |
| RegionMatrix | Region enrichment analysis |
| RegionMatrix.ChromatinAssay | Region enrichment analysis |
| RegionMatrix.default | Region enrichment analysis |
| RegionMatrix.Seurat | Region enrichment analysis |
| RegionPlot | Region plot |
| RegionStats | Compute base composition information for genomic ranges |
| RegionStats.ChromatinAssay | 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 |
| RunChromVAR.ChromatinAssay | Run chromVAR |
| RunChromVAR.Seurat | 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 |
| RunSVD.StdAssay | 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 |
| RunTFIDF.StdAssay | Compute the term-frequency inverse-document-frequency |
-- S --
| seqinfo | Access and modify sequence information for ChromatinAssay objects |
| seqinfo-method | Access and modify sequence information for ChromatinAssay objects |
| seqinfo-methods | Access and modify sequence information for ChromatinAssay objects |
| seqinfo<--method | Access and modify sequence information for ChromatinAssay objects |
| seqlengths | Access and modify sequence information for ChromatinAssay objects |
| seqlengths-method | Access and modify sequence information for ChromatinAssay objects |
| seqlengths<--method | Access and modify sequence information for ChromatinAssay objects |
| seqlevels | Access and modify sequence information for ChromatinAssay objects |
| seqlevels-method | Access and modify sequence information for ChromatinAssay objects |
| seqlevels<--method | Access and modify sequence information for ChromatinAssay objects |
| seqnames | Access and modify sequence information for ChromatinAssay objects |
| seqnames-method | Access and modify sequence information for ChromatinAssay objects |
| seqnames<--method | Access and modify sequence information for ChromatinAssay objects |
| SetMotifData | Set motif data |
| SetMotifData.ChromatinAssay | Set motif data |
| SetMotifData.Motif | Set motif data |
| SetMotifData.Seurat | Set motif data |
| Signac | Signac: Analysis of Single-Cell Chromatin Data |
| SplitFragments | Split fragment file by cell identities |
| StringToGRanges | String to GRanges |
| subset.Fragment | Subset a Fragment object |
| subset.Motif | Subset a Motif object |
| SubsetMatrix | Subset matrix rows and columns |
-- T --
| theme_browser | Genome browser theme |
| TilePlot | Plot integration sites per cell |
| TSSEnrichment | Compute TSS enrichment score per cell |
| TSSPlot | Plot signal enrichment around TSSs |
-- U --
| UnifyPeaks | Unify genomic ranges |
| UpdatePath | Update the file path for a Fragment object |
-- V --
| ValidateCells | Validate cells present in fragment file |
| ValidateFragments | Validate Fragment object |
| ValidateHash | Validate hashes for Fragment object |
| VariantPlot | Plot strand concordance vs. VMR |
-- misc --
| [.Motif | Subset a Motif object |