Function reference • Signac

Object interaction Functions for interacting with a Signac classes
`Annotation()` `Annotation<-`()	Annotation
`ChromatinAssay-class`	The ChromatinAssay class
`CreateChromatinAssay()`	Create ChromatinAssay object
`Fragments()` `Fragments<-`()	Get the Fragment objects
`GetFragmentData()`	Get Fragment object data
`Links()` `Links<-`()	Get or set links information
`Motifs()` `Motifs<-`()	Get or set a motif information
`as.ChromatinAssay()`	Convert objects to a ChromatinAssay
Quantification and peak calling Functions for identifying and quantifying genomic regions
`AggregateTiles()`	Quantify aggregated genome tiles
`CallPeaks()`	Call peaks
`FeatureMatrix()`	Feature Matrix
`GenomeBinMatrix()`	Genome bin matrix
Preprocessing Functions for preprocessing single-cell data
`BinarizeCounts()`	Binarize counts
`CreateMotifMatrix()`	Create motif matrix
`DownsampleFeatures()`	Downsample Features
`FindTopFeatures()`	Find most frequently observed features
`RunTFIDF()`	Compute the term-frequency inverse-document-frequency
`UnifyPeaks()`	Unify genomic ranges
Quality control Functions for performing quality control
`FRiP()`	Calculate fraction of reads in peaks per cell
`FragmentHistogram()`	Plot fragment length histogram
`NucleosomeSignal()`	NucleosomeSignal
`TSSEnrichment()`	Compute TSS enrichment score per cell
`TSSPlot()`	Plot signal enrichment around TSSs
Dimension reduction Functions for reducing dimensions
`Jaccard()`	Calculate the Jaccard index between two matrices
`RunSVD()`	Run singular value decomposition
Visualization Functions for visualizing single-cell data
`AnnotationPlot()`	Plot gene annotations
`BigwigTrack()`	Plot data from BigWig
`CombineTracks()`	Combine genome region plots
`CoverageBrowser()`	Genome browser
`CoveragePlot()`	Plot Tn5 insertion frequency over a region
`DepthCor()`	Plot sequencing depth correlation
`ExpressionPlot()`	Plot gene expression
`FragmentHistogram()`	Plot fragment length histogram
`LinkPlot()`	Plot linked genomic elements
`MotifPlot()`	Plot DNA sequence motif
`PeakPlot()`	Plot peaks in a genomic region
`PlotFootprint()`	Plot motif footprinting results
`TSSPlot()`	Plot signal enrichment around TSSs
`TilePlot()`	Plot integration sites per cell
`VariantPlot()`	Plot strand concordance vs. VMR
`theme_browser()`	Genome browser theme
Utilities Utility functions for working with single-cell data
`AccessiblePeaks()`	Accessible peaks
`AddChromatinModule()`	Add chromatin module
`AverageCounts()`	Average Counts
`CellsPerGroup()`	Cells per group
`ClosestFeature()`	Closest Feature
`CountsInRegion()`	Counts in region
`Extend()`	Extend
`FoldChange()`	Compute fold change between two groups of cells
`FractionCountsInRegion()`	Fraction of counts in a genomic region
`GRangesToString()`	GRanges to String
`GeneActivity()`	Create gene activity matrix
`GetCellsInRegion()`	Get cells in a region
`GetGRangesFromEnsDb()`	Extract genomic ranges from EnsDb object
`GetIntersectingFeatures()`	Find intersecting regions between two objects
`GetTSSPositions()`	Find transcriptional start sites
`IntersectMatrix()`	Intersect genomic coordinates with matrix rows
`LookupGeneCoords()`	Get gene coordinates
`MatchRegionStats()`	Match DNA sequence characteristics
`StringToGRanges()`	String to GRanges
`SubsetMatrix()`	Subset matrix rows and columns
`UnifyPeaks()`	Unify genomic ranges
Footprinting Functions for performing TF footprinting
`Footprint()`	Transcription factor footprinting analysis
`GetFootprintData()`	Get footprinting data
`InsertionBias()`	Compute Tn5 insertion bias
`PlotFootprint()`	Plot motif footprinting results
Motif analysis Functions for performing DNA sequence motif analysis
`AddMotifs()`	Add DNA sequence motif information
`ConvertMotifID()`	Convert between motif name and motif ID
`CreateMotifMatrix()`	Create motif matrix
`CreateMotifObject()`	Create motif object
`FindMotifs()`	FindMotifs
`GetMotifData()`	Retrieve a motif matrix
`MatchRegionStats()`	Match DNA sequence characteristics
`Motif-class`	The Motif class
`MotifPlot()`	Plot DNA sequence motif
`Motifs()` `Motifs<-`()	Get or set a motif information
`RegionStats()`	Compute base composition information for genomic ranges
`RunChromVAR()`	Run chromVAR
`SetMotifData()`	Set motif data
`subset(<Motif>)` `[`(<Motif>)	Subset a Motif object
Mitochondrial lineage tracing Functions for identifying cell lineages or clonotypes from mitochondrial mutations
`AlleleFreq()`	Compute allele frequencies per cell
`ClusterClonotypes()`	Find relationships between clonotypes
`FindClonotypes()`	Find clonotypes
`IdentifyVariants()`	Identify mitochondrial variants
`ReadMGATK()`	Read MGATK output
`VariantPlot()`	Plot strand concordance vs. VMR
Fragments Functions for working with fragment files
`Cells(<Fragment>)` `Cells<-`(<Fragment>)	Set and get cell barcode information for a `Fragment` object
`CountFragments()`	Count fragments
`CreateFragmentObject()`	Create a Fragment object
`FilterCells()`	Filter cells from fragment file
`Fragment-class`	The Fragment class
`Fragments()` `Fragments<-`()	Get the Fragment objects
`SplitFragments()`	Split fragment file by cell identities
`UpdatePath()`	Update the file path for a Fragment object
`ValidateCells()`	Validate cells present in fragment file
`ValidateFragments()`	Validate Fragment object
`ValidateHash()`	Validate hashes for Fragment object
Links Functions for working with genomic links
`ConnectionsToLinks()`	Cicero connections to links
`GetLinkedGenes()`	Get genes linked to peaks
`GetLinkedPeaks()`	Get peaks linked to genes
`LinkPeaks()`	Link peaks to genes
`LinkPlot()`	Plot linked genomic elements
`Links()` `Links<-`()	Get or set links information
Nearest methods Nearest genomic range methods for Signac-defined classes
`precede(<ANY>,<ChromatinAssay>)` `precede(<ChromatinAssay>,<ANY>)` `precede(<ChromatinAssay>,<ChromatinAssay>)` `precede(<ANY>,<Seurat>)` `precede(<Seurat>,<ANY>)` `precede(<Seurat>,<Seurat>)` `follow(<ANY>,<ChromatinAssay>)` `follow(<ChromatinAssay>,<ANY>)` `follow(<ChromatinAssay>,<ChromatinAssay>)` `follow(<ANY>,<Seurat>)` `follow(<Seurat>,<ANY>)` `follow(<Seurat>,<Seurat>)` `nearest(<ANY>,<ChromatinAssay>)` `nearest(<ChromatinAssay>,<ANY>)` `nearest(<ChromatinAssay>,<ChromatinAssay>)` `nearest(<ANY>,<Seurat>)` `nearest(<Seurat>,<ANY>)` `nearest(<Seurat>,<Seurat>)` `distance(<ANY>,<ChromatinAssay>)` `distance(<ChromatinAssay>,<ANY>)` `distance(<ChromatinAssay>,<ChromatinAssay>)` `distance(<ANY>,<Seurat>)` `distance(<Seurat>,<ANY>)` `distance(<Seurat>,<Seurat>)` `distanceToNearest(<ANY>,<ChromatinAssay>)` `distanceToNearest(<ChromatinAssay>,<ANY>)` `distanceToNearest(<ChromatinAssay>,<ChromatinAssay>)` `distanceToNearest(<ANY>,<Seurat>)` `distanceToNearest(<Seurat>,<ANY>)` `distanceToNearest(<Seurat>,<Seurat>)`	Find the nearest range neighbors for ChromatinAssay objects
Inter-range methods Inter-range methods for Signac-defined classes
`range(<ChromatinAssay>)` `range(<Seurat>)` `reduce(<ChromatinAssay>)` `reduce(<Seurat>)` `gaps(<ChromatinAssay>)` `gaps(<Seurat>)` `disjoin(<ChromatinAssay>)` `disjoin(<Seurat>)` `isDisjoint(<ChromatinAssay>)` `isDisjoint(<Seurat>)` `disjointBins(<ChromatinAssay>)` `disjointBins(<Seurat>)`	Inter-range transformations for ChromatinAssay objects
Overlap methods Overlap-range methods for Signac-defined classes
`findOverlaps(<Vector>,<ChromatinAssay>)` `findOverlaps(<ChromatinAssay>,<Vector>)` `findOverlaps(<ChromatinAssay>,<ChromatinAssay>)` `findOverlaps(<Vector>,<Seurat>)` `findOverlaps(<Seurat>,<Vector>)` `findOverlaps(<Seurat>,<Seurat>)` `countOverlaps(<Vector>,<ChromatinAssay>)` `countOverlaps(<ChromatinAssay>,<Vector>)` `countOverlaps(<ChromatinAssay>,<ChromatinAssay>)` `countOverlaps(<Seurat>,<Vector>)` `countOverlaps(<Vector>,<Seurat>)` `countOverlaps(<Seurat>,<Seurat>)`	Find overlapping ranges for ChromatinAssay objects
Coverage methods Genomic range coverage methods for Signac-defined classes
`coverage(<ChromatinAssay>)` `coverage(<Seurat>)`	Coverage of a ChromatinAssay object
Genomic range methods Genomic ranges methods for Signac-defined classes
`granges(<ChromatinAssay>)` `granges(<Seurat>)`	Access genomic ranges for ChromatinAssay objects
Seqinfo methods Seqinfo methods for Signac-defined classes
`seqinfo(<ChromatinAssay>)` `seqinfo<-`(<ChromatinAssay>) `seqlevels(<ChromatinAssay>)` `seqlevels<-`(<ChromatinAssay>) `seqnames(<ChromatinAssay>)` `seqnames<-`(<ChromatinAssay>) `seqlengths(<ChromatinAssay>)` `seqlengths<-`(<ChromatinAssay>) `genome(<ChromatinAssay>)` `genome<-`(<ChromatinAssay>) `isCircular(<ChromatinAssay>)` `isCircular<-`(<ChromatinAssay>) `seqinfo(<Seurat>)` `seqinfo<-`(<Seurat>) `seqlevels(<Seurat>)` `seqlevels<-`(<Seurat>) `seqnames(<Seurat>)` `seqnames<-`(<Seurat>) `seqlengths(<Seurat>)` `seqlengths<-`(<Seurat>) `genome(<Seurat>)` `genome<-`(<Seurat>) `isCircular(<Seurat>)` `isCircular<-`(<Seurat>)	Access and modify sequence information for ChromatinAssay objects
Data Datasets included in Signac
`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_hg38_unified`	Unified genomic blacklist regions for Human GRCh38
`blacklist_mm10`	Genomic blacklist regions for Mouse mm10

Reference

Object interaction

Quantification and peak calling

Preprocessing

Quality control

Dimension reduction

Visualization

Utilities

Footprinting

Motif analysis

Mitochondrial lineage tracing

Fragments

Links

Nearest methods

Inter-range methods

Overlap methods

Coverage methods

Genomic range methods

Seqinfo methods

Data