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:
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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
- 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
Last updated 26 days agofrom:0b33b1154f. Checks:OK: 8 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 22 2024 |
| R-4.5-win-x86_64 | OK | Aug 22 2024 |
| R-4.5-linux-x86_64 | OK | Aug 22 2024 |
| R-4.4-win-x86_64 | OK | Aug 22 2024 |
| R-4.4-mac-x86_64 | OK | Aug 22 2024 |
| R-4.4-mac-aarch64 | OK | Aug 22 2024 |
| R-4.3-win-x86_64 | OK | Aug 22 2024 |
| R-4.3-mac-x86_64 | OK | Aug 22 2024 |
| R-4.3-mac-aarch64 | NOTE | Aug 22 2024 |
Exports:AccessiblePeaksAddChromatinModuleAddMotifsAggregateTilesAlleleFreqAnnotationAnnotation<-AnnotationPlotas.ChromatinAssayAverageCountsBigwigTrackBinarizeCountsCallPeaksCellsCells<-CellsPerGroupClosestFeatureClusterClonotypesCombineTracksConnectionsToLinksConvertMotifIDcorSparseCountFragmentsCountsInRegioncoverageCoverageBrowserCoveragePlotCreateChromatinAssayCreateFragmentObjectCreateMotifMatrixCreateMotifObjectDensityScatterDepthCordisjoindisjointBinsdistancedistanceToNearestDownsampleFeaturesExpressionPlotExtendFeatureMatrixFilterCellsFindClonotypesFindMotifsfindOverlapsFindTopFeaturesfollowFootprintFractionCountsInRegionFragmentHistogramFragmentsFragments<-FRiPgapsGeneActivitygenomegenome<-GenomeBinMatrixGetCellsInRegionGetFootprintDataGetFragmentDataGetGRangesFromEnsDbGetIntersectingFeaturesGetLinkedGenesGetLinkedPeaksGetMotifDataGetTSSPositionsgrangesGRangesToStringIdentifyVariantsInsertionBiasIntersectMatrixisCircularisCircular<-isDisjointJaccardLinkPeaksLinkPlotLinksLinks<-LookupGeneCoordsMatchRegionStatsMotifCountsMotifPlotMotifsMotifs<-nearestNucleosomeSignalPeakPlotPlotFootprintprecedeReadMGATKreduceRegionHeatmapRegionMatrixRegionPlotRegionStatsRunChromVARRunSVDRunTFIDFseqinfoseqinfo<-seqlengthsseqlengths<-seqlevelsseqlevels<-seqnamesseqnames<-SetMotifDataSortIdentsSplitFragmentsStringToGRangesSubsetMatrixtheme_browserTilePlotTSSEnrichmentTSSPlotUnifyPeaksUpdatePathValidateCellsValidateFragmentsValidateHashVariantPlot
Dependencies:askpassBHBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurldata.tabledigestdotCall64dplyrfansifarverfastmatchformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegtablehttrIRangesirlbaisobandjsonlitelabelinglambda.rlatticelifecyclelistenvmagrittrMASSMatrixmgcvmimemunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigprogressrpurrrR6RColorBrewerRcppRcppEigenRcppRollRhtslibrlangRsamtoolsS4VectorsscalesSeuratObjectsnowspspamstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
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 |
