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

Preprocessing

Functions for preprocessing single-cell data

BinarizeCounts()

Binarize counts

CreateMotifMatrix()

Create motif matrix

DownsampleFeatures()

Downsample Features

FeatureMatrix()

Feature Matrix

FindTopFeatures()

Find most frequently observed features

GenomeBinMatrix()

Genome bin matrix

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

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

FeatureMatrix()

Feature Matrix

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

GenomeBinMatrix()

Genome bin matrix

GetCellsInRegion()

Get cells in a region

GetGRangesFromEnsDb()

Extract genomic ranges from EnsDb object

GetIntersectingFeatures()

Find interesecting 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

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

ValidateCells()

Validate cells present in fragment file

ValidateFragments()

Validate Fragment object

ValidateHash()

Validate hashes for Fragment object

Functions for working with genomic links

ConnectionsToLinks()

Cicero connections to links

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