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Signac 1.1.0

Signac is an extension of Seurat for the analysis of single-cell chromatin data.

Documentation can be found at https://satijalab.org/signac/

Install

# Install Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
setRepositories(ind=1:2)

# To install the current release
install.packages("Signac")

# To install the development version
install.packages("devtools")
devtools::install_github("timoast/signac", ref = "develop")

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Version

Install

install.packages('Signac')

Monthly Downloads

6,127

Version

1.1.1

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Tim Stuart

Last Published

February 3rd, 2021

Functions in Signac (1.1.1)

CoveragePlot

Plot Tn5 insertion frequency over a region
FoldChange

Compute fold change between two groups of cells
GetFragmentData

Get Fragment object data
FindTopFeatures

Find most frequently observed features
CountFragments

Count fragments
AddMotifs

Add DNA sequence motif information
Cells.Fragment

GenomeBinMatrix

Genome bin matrix
AggregateTiles

Quantify aggregated genome tiles
Cells<-

Set and get cell barcode information for a Fragment object
DownsampleFeatures

Downsample Features
CountsInRegion

Counts in region
GetGRangesFromEnsDb

Extract genomic ranges from EnsDb object
coverage,ChromatinAssay-method

Coverage of a ChromatinAssay object
AlleleFreq

Compute allele frequencies per cell
MatchRegionStats

Match DNA sequence characteristics
blacklist_ce11

Genomic blacklist regions for C. elegans ce11
CreateFragmentObject

Create a Fragment object
blacklist_ce10

Genomic blacklist regions for C. elegans ce10
CreateMotifMatrix

Create motif matrix
GeneActivity

Create gene activity matrix
ValidateHash

Validate hashes for Fragment object
Links

Get or set links information
LinkPeaks

Link peaks to genes
LinkPlot

Plot linked genomic elements
ExpressionPlot

Plot gene expression
SubsetMatrix

Subset matrix rows and columns
TSSEnrichment

Compute TSS enrichment score per cell
Jaccard

Calculate the Jaccard index between two matrices
FindClonotypes

Find clonotypes
FeatureMatrix

Feature Matrix
CoverageBrowser

Genome browser
GetFootprintData

Get footprinting data
FilterCells

Filter cells from fragment file
ClosestFeature

Closest Feature
UnifyPeaks

Unify genomic ranges
GetCellsInRegion

Get cells in a region
AverageCounts

Average Counts
ClusterClonotypes

Find relationships between clonotypes
GetLinkedPeaks

Get peaks linked to genes
PlotFootprint

Plot motif footprinting results
Fragment-class

The Fragment class
FindMotifs

FindMotifs
IntersectMatrix

Intersect genomic coordinates with matrix rows
RunTFIDF

Compute the term-frequency inverse-document-frequency
InsertionBias

Compute Tn5 insertion bias
Motif-class

The Motif class
FragmentHistogram

Plot fragment length histogram
MotifPlot

Plot DNA sequence motif
SetMotifData

Set motif data
Annotation

Annotation
CreateChromatinAssay

Create ChromatinAssay object
Motifs

Get or set a motif information
GetMotifData

Retrieve a motif matrix
NucleosomeSignal

NucleosomeSignal
inter-range-methods

Inter-range transformations for ChromatinAssay objects
findOverlaps-methods

Find overlapping ranges for ChromatinAssay objects
granges-methods

Access genomic ranges for ChromatinAssay objects
TSSPlot

Plot signal enrichment around TSSs
blacklist_hg38_unified

Unified genomic blacklist regions for Human GRCh38
TilePlot

Plot integration sites per cell
VariantPlot

Plot strand concordance vs. VMR
FractionCountsInRegion

Fraction of counts in a genomic region
IdentifyVariants

Identify mitochondrial variants
ReadMGATK

Read MGATK output
GetTSSPositions

Find transcriptional start sites
Fragments

Get the Fragment objects
RegionStats

Compute base composition information for genomic ranges
Footprint

Transcription factor footprinting analysis
GRangesToString

GRanges to String
blacklist_dm3

Genomic blacklist regions for Drosophila dm3
theme_browser

Genome browser theme
ValidateCells

Validate cells present in fragment file
ValidateFragments

Validate Fragment object
GetIntersectingFeatures

Find intersecting regions between two objects
GetLinkedGenes

Get genes linked to peaks
RunSVD

Run singular value decomposition
PeakPlot

Plot peaks in a genomic region
blacklist_hg19

Genomic blacklist regions for Human hg19
nearest-methods

Find the nearest range neighbors for ChromatinAssay objects
RunChromVAR

Run chromVAR
UpdatePath

Update the file path for a Fragment object
reexports

Objects exported from other packages
blacklist_mm10

Genomic blacklist regions for Mouse mm10
blacklist_hg38

Genomic blacklist regions for Human GRCh38
blacklist_dm6

Genomic blacklist regions for Drosophila dm6
seqinfo-methods

Access and modify sequence information for ChromatinAssay objects
subset.Motif

Subset a Motif object
CellsPerGroup

Cells per group
FRiP

Calculate fraction of reads in peaks per cell
DepthCor

Plot sequencing depth correlation
CreateMotifObject

Create motif object
SplitFragments

Split fragment file by cell identities
ChromatinAssay-class

The ChromatinAssay class
atac_small

A small example scATAC-seq dataset
Extend

Extend
LookupGeneCoords

Get gene coordinates
StringToGRanges

String to GRanges
as.ChromatinAssay

Convert objects to a ChromatinAssay
AnnotationPlot

Plot gene annotations
AccessiblePeaks

Accessible peaks
BinarizeCounts

Binarize counts
AddChromatinModule

Add chromatin module
CombineTracks

Combine genome region plots
CallPeaks

Call peaks
ConnectionsToLinks

Cicero connections to links
ConvertMotifID

Convert between motif name and motif ID