# Analysis of Single-Cell Chromatin Data

## Documentation for package ‘Signac’ version 1.17.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A B C D E F G H I J L M N P R S T U V misc

## -- A --

AccessiblePeaks | Accessible peaks
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
ATACqc | Compute scATAC-seq QC metrics
ATACqc.ChromatinAssay | Compute scATAC-seq QC metrics
ATACqc.default | Compute scATAC-seq QC metrics
ATACqc.Seurat | Compute scATAC-seq QC metrics
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 --

EnrichedTerms | Find enriched ontology terms
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
FitMeanVar | Find variable features fitting LOESS
FitMeanVar.Assay | Find variable features fitting LOESS
FitMeanVar.data.frame | Find variable features fitting LOESS
FitMeanVar.default | Find variable features fitting LOESS
FitMeanVar.Seurat | Find variable features fitting LOESS
FitMeanVar.StdAssay | Find variable features fitting LOESS
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
PearsonResidualVar | Compute analytic Pearson residual variance
PearsonResidualVar.Assay | Compute analytic Pearson residual variance
PearsonResidualVar.default | Compute analytic Pearson residual variance
PearsonResidualVar.Seurat | Compute analytic Pearson residual variance
PearsonResidualVar.StdAssay | Compute analytic Pearson residual variance
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
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
SortIdents | Sorts cell metadata variable by similarity using hierarchical clustering
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