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]

Signac_1.14.0.tar.gz
Signac_1.14.0.tar.gz(r-4.5-noble)Signac_1.14.0.tar.gz(r-4.4-noble)
Signac_1.14.0.tgz(r-4.4-emscripten)
Signac.pdf |Signac.html✨
Signac/json (API)
NEWS

# Install 'Signac' in R:
install.packages('Signac', repos = 'https://cloud.r-project.org')

Bug tracker:https://github.com/stuart-lab/signac/issues37 issues

Pkgdown site:https://stuartlab.org

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

Conda:

zlibcpp

4.25 score 1 packages 5.9k downloads 24 mentions 123 exports 83 dependencies

Last updated 7 months agofrom:cfc15c5706. Checks:2 OK, 1 NOTE. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKMar 20 2025
R-4.5-linux-x86_64NOTEMar 20 2025
R-4.4-linux-x86_64OKMar 20 2025

Exports:AccessiblePeaksAddChromatinModuleAddMotifsAggregateTilesAlleleFreqAnnotationAnnotation<-AnnotationPlotas.ChromatinAssayAverageCountsBigwigTrackBinarizeCountsCallPeaksCellsCells<-CellsPerGroupClosestFeatureClusterClonotypesCombineTracksConnectionsToLinksConvertMotifIDcorSparseCountFragmentsCountsInRegioncoverageCoverageBrowserCoveragePlotCreateChromatinAssayCreateFragmentObjectCreateMotifMatrixCreateMotifObjectDensityScatterDepthCordisjoindisjointBinsdistancedistanceToNearestDownsampleFeaturesExpressionPlotExtendFeatureMatrixFilterCellsFindClonotypesFindMotifsfindOverlapsFindTopFeaturesfollowFootprintFractionCountsInRegionFragmentHistogramFragmentsFragments<-FRiPgapsGeneActivitygenomegenome<-GenomeBinMatrixGetCellsInRegionGetFootprintDataGetFragmentDataGetGRangesFromEnsDbGetIntersectingFeaturesGetLinkedGenesGetLinkedPeaksGetMotifDataGetTSSPositionsgrangesGRangesToStringIdentifyVariantsInsertionBiasIntersectMatrixisCircularisCircular<-isDisjointJaccardLinkPeaksLinkPlotLinksLinks<-LookupGeneCoordsMatchRegionStatsMotifCountsMotifPlotMotifsMotifs<-nearestNucleosomeSignalPeakPlotPlotFootprintprecedeReadMGATKreduceRegionHeatmapRegionMatrixRegionPlotRegionStatsRunChromVARRunSVDRunTFIDFseqinfoseqinfo<-seqlengthsseqlengths<-seqlevelsseqlevels<-seqnamesseqnames<-SetMotifDataSortIdentsSplitFragmentsStringToGRangesSubsetMatrixtheme_browserTilePlotTSSEnrichmentTSSPlotUnifyPeaksUpdatePathValidateCellsValidateFragmentsValidateHashVariantPlot

Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurldata.tabledigestdotCall64dplyrfansifarverfastmatchformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegtablehttrIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelistenvmagrittrMASSMatrixmgcvmimemunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigprogressrpurrrR6RColorBrewerRcppRcppEigenRcppRollRhtslibrlangRsamtoolsS4VectorsscalesSeuratObjectsnowspspamstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVector

Citation

To cite Signac, please use:

Stuart et al. Single-cell chromatin state analysis with Signac. Nature Methods (2021).

Corresponding BibTeX entry: 

  @Article{,
    author = {Tim Stuart and Avi Srivastava and Shaista Madad and Caleb
      Lareau and Rahul Satija},
    title = {Single-cell chromatin state analysis with Signac},
    journal = {Nature Methods},
    year = {2021},
    doi = {10.1038/s41592-021-01282-5},
    note = {https://doi.org/10.1038/s41592-021-01282-5},
  }

Readme and manuals

Signac

Overview

Signac is a comprehensive R package for the analysis of single-cell chromatin data. Signac includes functions for quality control, normalization, dimension reduction, clustering, differential activity, and more.

Documentation and tutorials can be found at https://stuartlab.org/signac/

Installation

To install the latest release of Signac from CRAN:

setRepositories(ind=1:3) # needed to automatically install Bioconductor dependencies
install.packages("Signac")

To release the latest develop version from GitHub:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
remotes::install_github("stuart-lab/signac", ref = "develop")

Release notes

For a changelog please see the NEWS file, also available on the Signac website.

Contributing

We welcome contributions to the Signac package. Please see the contribution guide for more information.

Getting help

If you encounter a bug or have a feature request, please open an issue.

If you would like to discuss questions related to single-cell analysis, you can open a discussion.

Roadmap

Signac runs on a quarterly release schedule. Additional releases will be scheduled in the case of urgent bug fixes. The development roadmap can be viewed on GitHub here.

Citing Signac

If you use the Signac package in your work please cite Stuart et al. 2021

@ARTICLE{signac,
  title     = "Single-cell chromatin state analysis with Signac",
  author    = "Stuart, Tim and Srivastava, Avi and Madad, Shaista and Lareau,
               Caleb A and Satija, Rahul",
  journal   = "Nat. Methods",
  publisher = "Nature Publishing Group",
  pages     = "1--9",
  month     =  nov,
  year      =  2021,
  url       = "https://www.nature.com/articles/s41592-021-01282-5",
  language  = "en"
}

Related packages

Help Manual

Help pageTopics
Signac: Analysis of Single-Cell Chromatin DataSignac-package Signac
Accessible peaksAccessiblePeaks
Add chromatin moduleAddChromatinModule
Add DNA sequence motif informationAddMotifs AddMotifs.Assay AddMotifs.ChromatinAssay AddMotifs.default AddMotifs.Seurat AddMotifs.StdAssay
Quantify aggregated genome tilesAggregateTiles AggregateTiles.ChromatinAssay AggregateTiles.default AggregateTiles.Seurat
Compute allele frequencies per cellAlleleFreq AlleleFreq.Assay AlleleFreq.default AlleleFreq.Seurat AlleleFreq.StdAssay
AnnotationAnnotation Annotation.ChromatinAssay Annotation.Seurat Annotation<- Annotation<-.ChromatinAssay Annotation<-.Seurat
Plot gene annotationsAnnotationPlot
Convert objects to a ChromatinAssayas.ChromatinAssay as.ChromatinAssay.Assay
A small example scATAC-seq datasetatac_small
Average CountsAverageCounts
Plot data from BigWig filesBigwigTrack
Binarize countsBinarizeCounts 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 GRCh38blacklist_hg38
Unified genomic blacklist regions for Human GRCh38blacklist_hg38_unified
Genomic blacklist regions for Mouse mm10 (0-based)blacklist_mm10
Call peaksCallPeaks CallPeaks.ChromatinAssay CallPeaks.default CallPeaks.Fragment CallPeaks.Seurat
Set and get cell barcode information for a 'Fragment' objectCells.Fragment Cells<-.Fragment
Set and get cell barcode information for a Fragment objectCells<-
Cells per groupCellsPerGroup
The ChromatinAssay classChromatinAssay ChromatinAssay-class
Closest FeatureClosestFeature
Find relationships between clonotypesClusterClonotypes
Combine genome region plotsCombineTracks
Cicero connections to linksConnectionsToLinks
Convert between motif name and motif IDConvertMotifID ConvertMotifID.Assay ConvertMotifID.ChromatinAssay ConvertMotifID.default ConvertMotifID.Motif ConvertMotifID.Seurat ConvertMotifID.StdAssay
Count fragmentsCountFragments
Counts in regionCountsInRegion
Coverage of a ChromatinAssay objectcoverage coverage,ChromatinAssay-method coverage,Seurat-method
Genome browserCoverageBrowser
Plot Tn5 insertion frequency over a regionCoveragePlot
Create ChromatinAssay objectCreateChromatinAssay
Create a Fragment objectCreateFragmentObject
Create motif matrixCreateMotifMatrix
Create motif objectCreateMotifObject
Scatterplot colored by point densityDensityScatter
Plot sequencing depth correlationDepthCor
Downsample FeaturesDownsampleFeatures
Plot gene expressionExpressionPlot
ExtendExtend
Feature MatrixFeatureMatrix
Filter cells from fragment fileFilterCells
Find clonotypesFindClonotypes
FindMotifsFindMotifs
Find overlapping ranges for ChromatinAssay objectscountOverlaps 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 featuresFindTopFeatures FindTopFeatures.Assay FindTopFeatures.default FindTopFeatures.Seurat FindTopFeatures.StdAssay
Transcription factor footprinting analysisFootprint Footprint.ChromatinAssay Footprint.Seurat
Fraction of counts in a genomic regionFractionCountsInRegion
The Fragment classFragment Fragment-class
Plot fragment length histogramFragmentHistogram
Get the Fragment objectsFragments Fragments.ChromatinAssay Fragments.Seurat Fragments<- Fragments<-.ChromatinAssay Fragments<-.Seurat
Calculate fraction of reads in peaks per cellFRiP
Create gene activity matrixGeneActivity
Genome bin matrixGenomeBinMatrix
Get cells in a regionGetCellsInRegion
Get footprinting dataGetFootprintData
Get Fragment object dataGetFragmentData
Extract genomic ranges from EnsDb objectGetGRangesFromEnsDb
Find intersecting regions between two objectsGetIntersectingFeatures
Get genes linked to peaksGetLinkedGenes
Get peaks linked to genesGetLinkedPeaks
Retrieve a motif matrixGetMotifData GetMotifData.ChromatinAssay GetMotifData.Motif GetMotifData.Seurat
Find transcriptional start sitesGetTSSPositions
Access genomic ranges for ChromatinAssay objectsgranges granges,ChromatinAssay-method granges,Seurat-method granges-methods
GRanges to StringGRangesToString
Return the first rows of a fragment filehead.Fragment
Identify mitochondrial variantsIdentifyVariants IdentifyVariants.Assay IdentifyVariants.default IdentifyVariants.Seurat IdentifyVariants.StdAssay
Compute Tn5 insertion biasInsertionBias InsertionBias.ChromatinAssay InsertionBias.Seurat
Inter-range transformations for ChromatinAssay objectsdisjoin 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 rowsIntersectMatrix
Calculate the Jaccard index between two matricesJaccard
Link peaks to genesLinkPeaks
Plot linked genomic elementsLinkPlot
Get or set links informationLinks Links.ChromatinAssay Links.Seurat Links<- Links<-.ChromatinAssay Links<-.Seurat
Get gene coordinatesLookupGeneCoords
Match DNA sequence characteristicsMatchRegionStats
The Motif classMotif Motif-class
Count fragments surrounding motif sitesMotifCounts
Plot DNA sequence motifMotifPlot
Get or set a motif informationMotifs Motifs.ChromatinAssay Motifs.Seurat Motifs<- Motifs<-.ChromatinAssay Motifs<-.Seurat
Find the nearest range neighbors for ChromatinAssay objectsdistance 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
NucleosomeSignalNucleosomeSignal
Plot peaks in a genomic regionPeakPlot
Plot motif footprinting resultsPlotFootprint
Read MGATK outputReadMGATK
Region heatmapRegionHeatmap
Region enrichment analysisRegionMatrix RegionMatrix.ChromatinAssay RegionMatrix.default RegionMatrix.Seurat
Region plotRegionPlot
Compute base composition information for genomic rangesRegionStats RegionStats.ChromatinAssay RegionStats.default RegionStats.Seurat
Run chromVARRunChromVAR RunChromVAR.ChromatinAssay RunChromVAR.Seurat
Run singular value decompositionRunSVD RunSVD.Assay RunSVD.default RunSVD.Seurat RunSVD.StdAssay
Compute the term-frequency inverse-document-frequencyRunTFIDF RunTFIDF.Assay RunTFIDF.default RunTFIDF.Seurat RunTFIDF.StdAssay
Access and modify sequence information for ChromatinAssay objectsgenome 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 dataSetMotifData SetMotifData.ChromatinAssay SetMotifData.Motif SetMotifData.Seurat
Sorts cell metadata variable by similarity using hierarchical clusteringSortIdents
Split fragment file by cell identitiesSplitFragments
String to GRangesStringToGRanges
Subset a Fragment objectsubset.Fragment
Subset a Motif objectsubset.Motif [.Motif
Subset matrix rows and columnsSubsetMatrix
Genome browser themetheme_browser
Plot integration sites per cellTilePlot
Compute TSS enrichment score per cellTSSEnrichment
Plot signal enrichment around TSSsTSSPlot
Unify genomic rangesUnifyPeaks
Update the file path for a Fragment objectUpdatePath
Validate cells present in fragment fileValidateCells
Validate Fragment objectValidateFragments
Validate hashes for Fragment objectValidateHash
Plot strand concordance vs. VMRVariantPlot