Package: Signac 1.14.0

Tim Stuart

Signac: Analysis of Single-Cell Chromatin Data

A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.

Authors:Tim Stuart [aut, cre], Avi Srivastava [aut], Paul Hoffman [ctb], Rahul Satija [ctb]

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Signac.pdf |Signac.html✨
Signac/json (API)
NEWS

# Install 'Signac' in R:

install.packages('Signac', repos = c('https://stuart-lab.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stuart-lab/signac/issues

Uses libs:

zlib– Compression library
c++– GNU Standard C++ Library v3

Datasets:

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

On CRAN:

atac bioinformatics single-cell

12.31 score 329 stars 1 packages 3.5k scripts 6.5k downloads 24 mentions 123 exports 84 dependencies

Last updated 3 months agofrom:0b33b1154f. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 20 2024
R-4.5-win-x86_64	OK	Nov 20 2024
R-4.5-linux-x86_64	OK	Nov 20 2024
R-4.4-win-x86_64	OK	Nov 20 2024
R-4.4-mac-x86_64	OK	Nov 20 2024
R-4.4-mac-aarch64	OK	Nov 20 2024
R-4.3-win-x86_64	OK	Nov 20 2024
R-4.3-mac-x86_64	OK	Nov 20 2024
R-4.3-mac-aarch64	OK	Oct 21 2024

Exports:AccessiblePeaks AddChromatinModule AddMotifs AggregateTiles AlleleFreq Annotation Annotation<-AnnotationPlot as.ChromatinAssay AverageCounts BigwigTrack BinarizeCounts CallPeaks Cells Cells<-CellsPerGroup ClosestFeature ClusterClonotypes CombineTracks ConnectionsToLinks ConvertMotifID corSparse CountFragments CountsInRegion coverage CoverageBrowser CoveragePlot CreateChromatinAssay CreateFragmentObject CreateMotifMatrix CreateMotifObject DensityScatter DepthCor disjoin disjointBins distance distanceToNearest DownsampleFeatures ExpressionPlot Extend FeatureMatrix FilterCells FindClonotypes FindMotifs findOverlaps FindTopFeatures follow Footprint FractionCountsInRegion FragmentHistogram Fragments Fragments<-FRiP gaps GeneActivity genome genome<-GenomeBinMatrix GetCellsInRegion GetFootprintData GetFragmentData GetGRangesFromEnsDb GetIntersectingFeatures GetLinkedGenes GetLinkedPeaks GetMotifData GetTSSPositions granges GRangesToString IdentifyVariants InsertionBias IntersectMatrix isCircular isCircular<-isDisjoint Jaccard LinkPeaks LinkPlot Links Links<-LookupGeneCoords MatchRegionStats MotifCounts MotifPlot Motifs Motifs<-nearest NucleosomeSignal PeakPlot PlotFootprint precede ReadMGATK reduce RegionHeatmap RegionMatrix RegionPlot RegionStats RunChromVAR RunSVD RunTFIDF seqinfo seqinfo<-seqlengths seqlengths<-seqlevels seqlevels<-seqnames seqnames<-SetMotifData SortIdents SplitFragments StringToGRanges SubsetMatrix theme_browser TilePlot TSSEnrichment TSSPlot UnifyPeaks UpdatePath ValidateCells ValidateFragments ValidateHash VariantPlot

Dependencies:askpass BH BiocGenerics BiocParallel Biostrings bitops cli codetools colorspace cpp11 crayon curl data.table digest dotCall64 dplyr fansi farver fastmatch formatR futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 globals glue gtable httr IRanges irlba isoband jsonlite labeling lambda.r lattice lifecycle listenv magrittr MASS Matrix mgcv mime munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig progressr purrr R6 RColorBrewer Rcpp RcppEigen RcppRoll Rhtslib rlang Rsamtools S4Vectors scales SeuratObject snow sp spam stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Signac: Analysis of Single-Cell Chromatin Data	Signac-package Signac
Accessible peaks	AccessiblePeaks
Add chromatin module	AddChromatinModule
Add DNA sequence motif information	AddMotifs AddMotifs.Assay AddMotifs.ChromatinAssay AddMotifs.default AddMotifs.Seurat AddMotifs.StdAssay
Quantify aggregated genome tiles	AggregateTiles AggregateTiles.ChromatinAssay AggregateTiles.default AggregateTiles.Seurat
Compute allele frequencies per cell	AlleleFreq AlleleFreq.Assay AlleleFreq.default AlleleFreq.Seurat AlleleFreq.StdAssay
Annotation	Annotation Annotation.ChromatinAssay Annotation.Seurat Annotation<- Annotation<-.ChromatinAssay Annotation<-.Seurat
Plot gene annotations	AnnotationPlot
Convert objects to a ChromatinAssay	as.ChromatinAssay as.ChromatinAssay.Assay
A small example scATAC-seq dataset	atac_small
Average Counts	AverageCounts
Plot data from BigWig files	BigwigTrack
Binarize counts	BinarizeCounts BinarizeCounts.Assay BinarizeCounts.default BinarizeCounts.Seurat
Genomic blacklist regions for C. elegans ce10 (0-based)	blacklist_ce10
Genomic blacklist regions for C. elegans ce11 (0-based)	blacklist_ce11
Genomic blacklist regions for Drosophila dm3 (0-based)	blacklist_dm3
Genomic blacklist regions for Drosophila dm6 (0-based)	blacklist_dm6
Genomic blacklist regions for Human hg19 (0-based)	blacklist_hg19
Genomic blacklist regions for Human GRCh38	blacklist_hg38
Unified genomic blacklist regions for Human GRCh38	blacklist_hg38_unified
Genomic blacklist regions for Mouse mm10 (0-based)	blacklist_mm10
Call peaks	CallPeaks CallPeaks.ChromatinAssay CallPeaks.default CallPeaks.Fragment CallPeaks.Seurat
Set and get cell barcode information for a 'Fragment' object	Cells.Fragment Cells<-.Fragment
Set and get cell barcode information for a Fragment object	Cells<-
Cells per group	CellsPerGroup
The ChromatinAssay class	ChromatinAssay ChromatinAssay-class
Closest Feature	ClosestFeature
Find relationships between clonotypes	ClusterClonotypes
Combine genome region plots	CombineTracks
Cicero connections to links	ConnectionsToLinks
Convert between motif name and motif ID	ConvertMotifID ConvertMotifID.Assay ConvertMotifID.ChromatinAssay ConvertMotifID.default ConvertMotifID.Motif ConvertMotifID.Seurat ConvertMotifID.StdAssay
Count fragments	CountFragments
Counts in region	CountsInRegion
Coverage of a ChromatinAssay object	coverage coverage,ChromatinAssay-method coverage,Seurat-method
Genome browser	CoverageBrowser
Plot Tn5 insertion frequency over a region	CoveragePlot
Create ChromatinAssay object	CreateChromatinAssay
Create a Fragment object	CreateFragmentObject
Create motif matrix	CreateMotifMatrix
Create motif object	CreateMotifObject
Scatterplot colored by point density	DensityScatter
Plot sequencing depth correlation	DepthCor
Downsample Features	DownsampleFeatures
Plot gene expression	ExpressionPlot
Extend	Extend
Feature Matrix	FeatureMatrix
Filter cells from fragment file	FilterCells
Find clonotypes	FindClonotypes
FindMotifs	FindMotifs
Find overlapping ranges for ChromatinAssay objects	countOverlaps countOverlaps,ChromatinAssay,ChromatinAssay-method countOverlaps,ChromatinAssay,Vector-method countOverlaps,Seurat,Seurat-method countOverlaps,Seurat,Vector-method countOverlaps,Vector,ChromatinAssay-method countOverlaps,Vector,Seurat-method findOverlaps findOverlaps,ChromatinAssay,ChromatinAssay-method findOverlaps,ChromatinAssay,Vector-method findOverlaps,Seurat,Seurat-method findOverlaps,Seurat,Vector-method findOverlaps,Vector,ChromatinAssay-method findOverlaps,Vector,Seurat-method findOverlaps-methods
Find most frequently observed features	FindTopFeatures FindTopFeatures.Assay FindTopFeatures.default FindTopFeatures.Seurat FindTopFeatures.StdAssay
Transcription factor footprinting analysis	Footprint Footprint.ChromatinAssay Footprint.Seurat
Fraction of counts in a genomic region	FractionCountsInRegion
The Fragment class	Fragment Fragment-class
Plot fragment length histogram	FragmentHistogram
Get the Fragment objects	Fragments Fragments.ChromatinAssay Fragments.Seurat Fragments<- Fragments<-.ChromatinAssay Fragments<-.Seurat
Calculate fraction of reads in peaks per cell	FRiP
Create gene activity matrix	GeneActivity
Genome bin matrix	GenomeBinMatrix
Get cells in a region	GetCellsInRegion
Get footprinting data	GetFootprintData
Get Fragment object data	GetFragmentData
Extract genomic ranges from EnsDb object	GetGRangesFromEnsDb
Find intersecting regions between two objects	GetIntersectingFeatures
Get genes linked to peaks	GetLinkedGenes
Get peaks linked to genes	GetLinkedPeaks
Retrieve a motif matrix	GetMotifData GetMotifData.ChromatinAssay GetMotifData.Motif GetMotifData.Seurat
Find transcriptional start sites	GetTSSPositions
Access genomic ranges for ChromatinAssay objects	granges granges,ChromatinAssay-method granges,Seurat-method granges-methods
GRanges to String	GRangesToString
Return the first rows of a fragment file	head.Fragment
Identify mitochondrial variants	IdentifyVariants IdentifyVariants.Assay IdentifyVariants.default IdentifyVariants.Seurat IdentifyVariants.StdAssay
Compute Tn5 insertion bias	InsertionBias InsertionBias.ChromatinAssay InsertionBias.Seurat
Inter-range transformations for ChromatinAssay objects	disjoin disjoin,ChromatinAssay-method disjoin,Seurat-method disjointBins disjointBins,ChromatinAssay-method disjointBins,Seurat-method gaps gaps,ChromatinAssay-method gaps,Seurat-method inter-range-methods isDisjoint isDisjoint,ChromatinAssay-method isDisjoint,Seurat-method range range,ChromatinAssay-method range,Seurat-method reduce reduce,ChromatinAssay-method reduce,Seurat-method
Intersect genomic coordinates with matrix rows	IntersectMatrix
Calculate the Jaccard index between two matrices	Jaccard
Link peaks to genes	LinkPeaks
Plot linked genomic elements	LinkPlot
Get or set links information	Links Links.ChromatinAssay Links.Seurat Links<- Links<-.ChromatinAssay Links<-.Seurat
Get gene coordinates	LookupGeneCoords
Match DNA sequence characteristics	MatchRegionStats
The Motif class	Motif Motif-class
Count fragments surrounding motif sites	MotifCounts
Plot DNA sequence motif	MotifPlot
Get or set a motif information	Motifs Motifs.ChromatinAssay Motifs.Seurat Motifs<- Motifs<-.ChromatinAssay Motifs<-.Seurat
Find the nearest range neighbors for ChromatinAssay objects	distance distance,ANY,ChromatinAssay-method distance,ANY,Seurat-method distance,ChromatinAssay,ANY-method distance,ChromatinAssay,ChromatinAssay-method distance,Seurat,ANY-method distance,Seurat,Seurat-method distanceToNearest distanceToNearest,ANY,ChromatinAssay-method distanceToNearest,ANY,Seurat-method distanceToNearest,ChromatinAssay,ANY-method distanceToNearest,ChromatinAssay,ChromatinAssay-method distanceToNearest,Seurat,ANY-method distanceToNearest,Seurat,Seurat-method follow follow,ANY,ChromatinAssay-method follow,ANY,Seurat-method follow,ChromatinAssay,ANY-method follow,ChromatinAssay,ChromatinAssay-method follow,Seurat,ANY-method follow,Seurat,Seurat-method nearest nearest,ANY,ChromatinAssay-method nearest,ANY,Seurat-method nearest,ChromatinAssay,ANY-method nearest,ChromatinAssay,ChromatinAssay-method nearest,Seurat,ANY-method nearest,Seurat,Seurat-method nearest-methods precede precede,ANY,ChromatinAssay-method precede,ANY,Seurat-method precede,ChromatinAssay,ANY-method precede,ChromatinAssay,ChromatinAssay-method precede,Seurat,ANY-method precede,Seurat,Seurat-method
NucleosomeSignal	NucleosomeSignal
Plot peaks in a genomic region	PeakPlot
Plot motif footprinting results	PlotFootprint
Read MGATK output	ReadMGATK
Region heatmap	RegionHeatmap
Region enrichment analysis	RegionMatrix RegionMatrix.ChromatinAssay RegionMatrix.default RegionMatrix.Seurat
Region plot	RegionPlot
Compute base composition information for genomic ranges	RegionStats RegionStats.ChromatinAssay RegionStats.default RegionStats.Seurat
Run chromVAR	RunChromVAR RunChromVAR.ChromatinAssay RunChromVAR.Seurat
Run singular value decomposition	RunSVD RunSVD.Assay RunSVD.default RunSVD.Seurat RunSVD.StdAssay
Compute the term-frequency inverse-document-frequency	RunTFIDF RunTFIDF.Assay RunTFIDF.default RunTFIDF.Seurat RunTFIDF.StdAssay
Access and modify sequence information for ChromatinAssay objects	genome genome,ChromatinAssay-method genome,Seurat-method genome<-,ChromatinAssay-method genome<-,Seurat-method isCircular isCircular,ChromatinAssay-method isCircular,Seurat-method isCircular<-,ChromatinAssay-method isCircular<-,Seurat-method seqinfo seqinfo,ChromatinAssay-method seqinfo,Seurat-method seqinfo-methods seqinfo<-,ChromatinAssay-method seqinfo<-,Seurat-method seqlengths seqlengths,ChromatinAssay-method seqlengths,Seurat-method seqlengths<-,ChromatinAssay-method seqlengths<-,Seurat-method seqlevels seqlevels,ChromatinAssay-method seqlevels,Seurat-method seqlevels<-,ChromatinAssay-method seqlevels<-,Seurat-method seqnames seqnames,ChromatinAssay-method seqnames,Seurat-method seqnames<-,ChromatinAssay-method seqnames<-,Seurat-method
Set motif data	SetMotifData SetMotifData.ChromatinAssay SetMotifData.Motif SetMotifData.Seurat
Sorts cell metadata variable by similarity using hierarchical clustering	SortIdents
Split fragment file by cell identities	SplitFragments
String to GRanges	StringToGRanges
Subset a Fragment object	subset.Fragment
Subset a Motif object	subset.Motif [.Motif
Subset matrix rows and columns	SubsetMatrix
Genome browser theme	theme_browser
Plot integration sites per cell	TilePlot
Compute TSS enrichment score per cell	TSSEnrichment
Plot signal enrichment around TSSs	TSSPlot
Unify genomic ranges	UnifyPeaks
Update the file path for a Fragment object	UpdatePath
Validate cells present in fragment file	ValidateCells
Validate Fragment object	ValidateFragments
Validate hashes for Fragment object	ValidateHash
Plot strand concordance vs. VMR	VariantPlot