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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

5,368

Version

1.1.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Maintainer

Tim Stuart

Last Published

November 7th, 2020

Functions in Signac (1.1.0)

CallPeaks

Call peaks
AddMotifs

Add DNA sequence motif information
Annotation

Annotation
AccessiblePeaks

Accessible peaks
AggregateTiles

Quantify aggregated genome tiles
AlleleFreq

Compute allele frequencies per cell
AnnotationPlot

Plot gene annotations
AverageCounts

Average Counts
BinarizeCounts

Binarize counts
CellsPerGroup

Cells per group
ConvertMotifID

Convert between motif name and motif ID
ExpressionPlot

Plot gene expression
DownsampleFeatures

Downsample Features
ConnectionsToLinks

Cicero connections to links
CombineTracks

Combine genome region plots
CoverageBrowser

Genome browser
Cells.Fragment

FeatureMatrix

Feature Matrix
CountsInRegion

Counts in region
Cells<-

Set and get cell barcode information for a Fragment object
CreateFragmentObject

Create a Fragment object
ChromatinAssay-class

The ChromatinAssay class
Extend

Extend
Fragments

Get the Fragment objects
FilterCells

Filter cells from fragment file
ClosestFeature

Closest Feature
AddChromatinModule

Add chromatin module
InsertionBias

Compute Tn5 insertion bias
LookupGeneCoords

Get gene coordinates
MatchRegionStats

Match DNA sequence characteristics
GRangesToString

GRanges to String
IntersectMatrix

Intersect genomic coordinates with matrix rows
FRiP

Calculate fraction of reads in peaks per cell
CreateMotifMatrix

Create motif matrix
CountFragments

Count fragments
FindClonotypes

Find clonotypes
GeneActivity

Create gene activity matrix
CoveragePlot

Plot Tn5 insertion frequency over a region
FindTopFeatures

Find most frequently observed features
ClusterClonotypes

Find relationships between clonotypes
CreateChromatinAssay

Create ChromatinAssay object
RunChromVAR

Run chromVAR
GetCellsInRegion

Get cells in a region
FindMotifs

FindMotifs
CreateMotifObject

Create motif object
GenomeBinMatrix

Genome bin matrix
DepthCor

Plot sequencing depth correlation
GetLinkedPeaks

Get peaks linked to genes
GetLinkedGenes

Get genes linked to peaks
LinkPlot

Plot linked genomic elements
GetFootprintData

Get footprinting data
GetIntersectingFeatures

Find interesecting regions between two objects
PeakPlot

Plot peaks in a genomic region
GetMotifData

Retrieve a motif matrix
Footprint

Transcription factor footprinting analysis
Fragment-class

The Fragment class
FractionCountsInRegion

Fraction of counts in a genomic region
PlotFootprint

Plot motif footprinting results
FoldChange

Compute fold change between two groups of cells
as.ChromatinAssay

Convert objects to a ChromatinAssay
RunSVD

Run singular value decomposition
atac_small

A small example scATAC-seq dataset
FragmentHistogram

Plot fragment length histogram
RunTFIDF

Compute the term-frequency inverse-document-frequency
SetMotifData

Set motif data
TSSPlot

Plot signal enrichment around TSSs
theme_browser

Genome browser theme
Links

Get or set links information
TilePlot

Plot integration sites per cell
GetTSSPositions

Find transcriptional start sites
SubsetMatrix

Subset matrix rows and columns
UnifyPeaks

Unify genomic ranges
Motifs

Get or set a motif information
StringToGRanges

String to GRanges
IdentifyVariants

Identify mitochondrial variants
SplitFragments

Split fragment file by cell identities
NucleosomeSignal

NucleosomeSignal
TSSEnrichment

Compute TSS enrichment score per cell
ValidateHash

Validate hashes for Fragment object
blacklist_dm6

Genomic blacklist regions for Drosophila dm6
blacklist_dm3

Genomic blacklist regions for Drosophila dm3
GetFragmentData

Get Fragment object data
coverage,ChromatinAssay-method

Coverage of a ChromatinAssay object
VariantPlot

Plot strand concordance vs. VMR
findOverlaps-methods

Find overlapping ranges for ChromatinAssay objects
blacklist_ce10

Genomic blacklist regions for C. elegans ce10
UpdatePath

Update the file path for a Fragment object
seqinfo-methods

Access and modify sequence information for ChromatinAssay objects
blacklist_hg38

Genomic blacklist regions for Human GRCh38
blacklist_ce11

Genomic blacklist regions for C. elegans ce11
blacklist_hg19

Genomic blacklist regions for Human hg19
nearest-methods

Find the nearest range neighbors for ChromatinAssay objects
granges-methods

Access genomic ranges for ChromatinAssay objects
GetGRangesFromEnsDb

Extract genomic ranges from EnsDb object
Jaccard

Calculate the Jaccard index between two matrices
subset.Motif

Subset a Motif object
inter-range-methods

Inter-range transformations for ChromatinAssay objects
MotifPlot

Plot DNA sequence motif
LinkPeaks

Link peaks to genes
RegionStats

Compute base composition information for genomic ranges
ValidateCells

Validate cells present in fragment file
reexports

Objects exported from other packages
ValidateFragments

Validate Fragment object
blacklist_mm10

Genomic blacklist regions for Mouse mm10
Motif-class

The Motif class
ReadMGATK

Read MGATK output
blacklist_hg38_unified

Unified genomic blacklist regions for Human GRCh38