Package index • Signac

Object interaction

Functions for interacting with a Signac classes

Annotation() `Annotation<-`(): Annotation
Bias() `Bias<-`(): Bias
`Cells<-`(): Set and get cell barcode information for a Fragment2 object
CreateGRangesAssay() CreateChromatinAssay5(): ChromatinAssay5 and GRangesAssay object constructors
Fragments() `Fragments<-`(): Get the Fragment objects
ChromatinAssay5-class GRangesAssay-class: ChromatinAssay5 and GRangesAssay object classes
GetFragmentData(): Get Fragment object data
Links() `Links<-`(): Get or set links information
Motifs() `Motifs<-`(): Get or set a motif information
RegionAggNames(): List stored RegionAggregation objects
RegionAggr() `RegionAggr<-`(): Region Aggregation
as.ChromatinAssay5(): Convert objects to a ChromatinAssay5 object
as.GRangesAssay(): Convert objects to a GRangesAssay object

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
RunFragtk(): Run fragtk matrix

Preprocessing

Functions for preprocessing single-cell data

BinarizeCounts(): Binarize counts
CreateMotifMatrix(): Create motif matrix
DownsampleFeatures(): Downsample Features
FindTopFeatures(): Find most frequently observed features
FitMeanVar(): Find variable features fitting LOESS
PearsonResidualVar(): Compute analytic Pearson residual variance
RunTFIDF(): Compute the term-frequency inverse-document-frequency

Quality control

Functions for performing quality control

ATACqc(): Compute scATAC-seq QC metrics
FRiP(): Calculate fraction of reads in peaks per cell
FragmentHistogram(): Plot fragment length histogram

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 files
CombineTracks(): Combine genome region plots
CoveragePlot(): Plot Tn5 insertion frequency over a region
DensityScatter(): Scatterplot colored by point density
DepthCor(): Plot sequencing depth correlation
ExpressionPlot(): Plot gene expression
FragmentHistogram(): Plot fragment length histogram
GWASTrack(): Create GWAS locus zoom track
LinkPlot(): Plot linked genomic elements
MotifPlot(): Plot DNA sequence motif
MultiCoveragePlot(): Plot multiple coverage plots
PeakPlot(): Plot peaks in a genomic region
PlotFootprint(): Plot motif footprinting results
RegionHeatmap(): Region heatmap
RegionPlot(): Region plot
TilePlot(): Plot integration sites per cell
VariantPlot(): Plot strand concordance vs. VMR
VariantTrack(): Plot variant positions
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
EnrichedTerms(): Find enriched ontology terms
Extend(): Extend
GeneActivity(): Create gene activity matrix
GetCellsInRegion(): Get cells in a region
GetGRangesFromEnsDb(): Extract genomic ranges from EnsDb object
GetTSSPositions(): Find transcriptional start sites
LookupGeneCoords(): Get gene coordinates
MatchRegionStats(): Match DNA sequence characteristics
SortIdents(): Sorts cell metadata variable by similarity using hierarchical clustering
SubsetMatrix(): Subset matrix rows and columns

Footprinting

Functions for performing TF footprinting

CreateRegionAggregationObject(): Create a RegionAggregation object
Footprint(): Transcription factor footprinting analysis
GetFootprintData(): Get footprinting data
InsertionBias(): Compute Tn5 insertion bias
PlotFootprint(): Plot motif footprinting results
RegionAggNames(): List stored RegionAggregation objects
RegionAggr() `RegionAggr<-`(): Region Aggregation
subset(<RegionAggregation>): RegionAggregation class

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

Heatmaps

Functions for single-cell heatmaps

RegionHeatmap(): Region heatmap
RegionMatrix(): Region enrichment analysis
RegionPlot(): Region plot

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
ReadMQuad(): Read MQuad output
VariantPlot(): Plot strand concordance vs. VMR

Fragments

Functions for working with fragment files

Cells(<Fragment2>) `Cells<-`(<Fragment2>): Set and get cell barcode information for a Fragment2 object
CountFragments(): Count fragments
CreateFragmentObject(): Create a Fragment object
FilterCells(): Filter cells from fragment file
seqlevels(<Fragment2>) `seqlevels<-`(<Fragment2>) seqlevelsStyle(<Fragment2>) `seqlevelsStyle<-`(<Fragment2>) renameSeqlevels(<Fragment2>): 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
as.Fragment2(): Convert objects to a Fragment2 object
head(<Fragment2>): Return the first rows of a fragment file
header(): Return the fragment file header
subset(<Fragment2>): Subset a 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
RegionAggr() `RegionAggr<-`(): Region Aggregation

GWAS

Functions for working with GWAS and QTL data

LoadCredibleSets(): Load fine-mapping credible sets
LoadGWAS(): Load GWAS-SSF file
LoadLDData(): Load LD data for a lead SNP

Nearest methods

Nearest genomic range methods for Signac-defined classes

precede(<ANY>,<GRangesAssay>) precede(<GRangesAssay>,<ANY>) precede(<GRangesAssay>,<GRangesAssay>) precede(<ANY>,<Seurat>) precede(<Seurat>,<ANY>) precede(<Seurat>,<Seurat>) follow(<ANY>,<GRangesAssay>) follow(<GRangesAssay>,<ANY>) follow(<GRangesAssay>,<GRangesAssay>) follow(<ANY>,<Seurat>) follow(<Seurat>,<ANY>) follow(<Seurat>,<Seurat>) nearest(<ANY>,<GRangesAssay>) nearest(<GRangesAssay>,<ANY>) nearest(<GRangesAssay>,<GRangesAssay>) nearest(<ANY>,<Seurat>) nearest(<Seurat>,<ANY>) nearest(<Seurat>,<Seurat>) distance(<ANY>,<GRangesAssay>) distance(<GRangesAssay>,<ANY>) distance(<GRangesAssay>,<GRangesAssay>) distance(<ANY>,<Seurat>) distance(<Seurat>,<ANY>) distance(<Seurat>,<Seurat>) distanceToNearest(<ANY>,<GRangesAssay>) distanceToNearest(<GRangesAssay>,<ANY>) distanceToNearest(<GRangesAssay>,<GRangesAssay>) distanceToNearest(<ANY>,<Seurat>) distanceToNearest(<Seurat>,<ANY>) distanceToNearest(<Seurat>,<Seurat>): Find the nearest range neighbors for GRangesAssay objects

Inter-range methods

Inter-range methods for Signac-defined classes

range(<GRangesAssay>) range(<Seurat>) reduce(<GRangesAssay>) reduce(<Seurat>) gaps(<GRangesAssay>) gaps(<Seurat>) disjoin(<GRangesAssay>) disjoin(<Seurat>) isDisjoint(<GRangesAssay>) isDisjoint(<Seurat>) disjointBins(<GRangesAssay>) disjointBins(<Seurat>): Inter-range transformations for GRangesAssay objects

Overlap methods

Overlap-range methods for Signac-defined classes

findOverlaps(<Vector>,<GRangesAssay>) findOverlaps(<GRangesAssay>,<Vector>) findOverlaps(<GRangesAssay>,<GRangesAssay>) findOverlaps(<Vector>,<Seurat>) findOverlaps(<Seurat>,<Vector>) findOverlaps(<Seurat>,<Seurat>) countOverlaps(<Vector>,<GRangesAssay>) countOverlaps(<GRangesAssay>,<Vector>) countOverlaps(<GRangesAssay>,<GRangesAssay>) countOverlaps(<Seurat>,<Vector>) countOverlaps(<Vector>,<Seurat>) countOverlaps(<Seurat>,<Seurat>): Find overlapping ranges for GRangesAssay objects

Coverage methods

Genomic range coverage methods for Signac-defined classes

coverage(<GRangesAssay>) coverage(<Seurat>): Coverage of a GRangesAssay object

Genomic range methods

Genomic ranges methods for Signac-defined classes

granges(<GRangesAssay>) granges(<Seurat>): Access genomic ranges for GRangesAssay objects

Seqinfo methods

Seqinfo methods for Signac-defined classes

seqinfo(<GRangesAssay>) seqlevels(<GRangesAssay>) seqnames(<GRangesAssay>) seqlengths(<GRangesAssay>) genome(<GRangesAssay>) isCircular(<GRangesAssay>) seqinfo(<Seurat>) seqlevels(<Seurat>) seqnames(<Seurat>) seqlengths(<Seurat>) genome(<Seurat>) isCircular(<Seurat>): Access and modify sequence information for GRangesAssay objects

Data

Datasets included in Signac

atac_small: A small example scATAC-seq dataset
atac_small_old: A small example scATAC-seq dataset (old)