Package: Seurat 4.4.0

Paul Hoffman

Seurat: Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Authors:Andrew Butler [ctb], Saket Choudhary [ctb], Charlotte Darby [ctb], Jeff Farrell [ctb], Christoph Hafemeister [ctb], Yuhan Hao [ctb], Austin Hartman [ctb], Paul Hoffman [aut, cre], Jaison Jain [ctb], Madeline Kowalski [ctb], Efthymia Papalexi [ctb], Patrick Roelli [ctb], Rahul Satija [ctb], Karthik Shekhar [ctb], Avi Srivastava [ctb], Tim Stuart [ctb], Kristof Torkenczy [ctb], Shiwei Zheng [ctb], Satija Lab and Collaborators [fnd]

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Seurat/json (API)
NEWS

# Install Seurat in R:
install.packages('Seurat', repos = c('https://satijalab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/satijalab/seurat/issues

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

On CRAN:

human-cell-atlassingle-cell-genomicssingle-cell-rna-seq

255 exports 2.2k stars 11.68 score 142 dependencies 97 dependents 73.2k downloads

Last updated 6 months agofrom:74905f1be2f14438e55b8cd3c96e89e6d13b4857 (via seurat4)

Exports:%||%%iff%AddAzimuthResultsAddMetaDataAddModuleScoreAggregateExpressionAnnotateAnchorsas.CellDataSetas.Graphas.Neighboras.Seuratas.SingleCellExperimentas.sparseAssaysAugmentPlotAutoPointSizeAverageExpressionBarcodeInflectionsPlotBGTextColorBlackAndWhiteBlueAndRedBoldTitleBuildClusterTreeCalcPerturbSigCalculateBarcodeInflectionsCaseMatchCellCycleScoringCellsCellsByIdentitiesCellScatterCellSelectorCenterTitleCollapseEmbeddingOutliersCollapseSpeciesExpressionMatrixColorDimSplitCombinePlotsCommandCreateAssayObjectCreateDimReducObjectCreateSCTAssayObjectCreateSeuratObjectCustomDistanceCustomPaletteDarkThemeDEenrichRPlotDefaultAssayDefaultAssay<-DietSeuratDimHeatmapDimPlotDiscretePaletteDistancesDoHeatmapDotPlotElbowPlotEmbeddingsExpMeanExpSDExpVarFastRowScaleFeatureLocatorFeaturePlotFeatureScatterFetchDataFilterSlideSeqFindAllMarkersFindClustersFindConservedMarkersFindIntegrationAnchorsFindMarkersFindMultiModalNeighborsFindNeighborsFindSpatiallyVariableFeaturesFindSubClusterFindTransferAnchorsFindVariableFeaturesFoldChangeFontSizeGeneSymbolThesarusGetAssayGetAssayDataGetImageGetIntegrationDataGetResidualGetTissueCoordinatesGetTransferPredictionsGroupCorrelationGroupCorrelationPlotHoverLocatorHTODemuxHTOHeatmapHVFInfoIdentsIdents<-IFeaturePlotImageDimPlotImageFeaturePlotImagesIndexIndex<-IndicesIntegrateDataIntegrateEmbeddingsIntensityIsGlobalISpatialDimPlotISpatialFeaturePlotJackStrawJackStrawPlotJSJS<-KeyKey<-L2CCAL2DimLabelClustersLabelPointsLinkedDimPlotLinkedFeaturePlotLoad10X_SpatialLoadAkoyaLoadAnnoyIndexLoadCurioSeekerLoadHuBMAPCODEXLoadingsLoadings<-LoadNanostringLoadSTARmapLoadVizgenLoadXeniumLocalStructLogNormalizeLogSeuratCommandLogVMRLuminanceMappingScoreMapQueryMetaFeatureMinMaxMiscMisc<-MixingMetricMixscapeHeatmapMixscapeLDAMULTIseqDemuxNeighborsNNPlotNoAxesNoGridNoLegendNormalizeDataPCAPlotPCASigGenesPCHeatmapPercentAbovePercentageFeatureSetPlotClusterTreePlotPerturbScorePolyDimPlotPolyFeaturePlotPredictAssayPrepLDAPrepSCTFindMarkersPrepSCTIntegrationProjectProject<-ProjectDimProjectUMAPPurpleAndYellowRadiusRead10XRead10X_h5Read10X_ImageRead10X_probe_metadataReadAkoyaReadMtxReadNanostringReadParseBioReadSlideSeqReadSTARsoloReadVitessceReadVizgenReadXeniumReductionsRegroupIdentsRelativeCountsRenameCellsRenameIdentsReorderIdentRestoreLegendRidgePlotRotatedAxisRowMergeSparseMatricesRunCCARunICARunLDARunMarkVarioRunMixscapeRunMoransIRunPCARunSLSIRunSPCARunTSNERunUMAPSampleUMISaveAnnoyIndexScaleDatascalefactorsScaleFactorsScoreJackStrawSCTransformSCTResultsSCTResults<-SelectIntegrationFeaturesSetAssayDataSetIdentSetIntegrationDataSetQuantileSeuratAxesSeuratThemeSingleCorPlotSingleDimPlotSingleExIPlotSingleImageMapSingleImagePlotSingleRasterMapSingleSpatialPlotSpatialDimPlotSpatialFeaturePlotSpatiallyVariableFeaturesSpatialPlotSpatialThemeSplitObjectStashIdentStdevSubsetByBarcodeInflectionsSVFInfoToolTool<-TopCellsTopFeaturesTopNeighborsTransferDataTSNEPlotUMAPPlotUpdateSCTAssaysUpdateSeuratObjectUpdateSymbolListVariableFeaturePlotVariableFeaturesVariableFeatures<-VizDimLoadingsVlnPlotWhichCellsWhiteBackground

Dependencies:abindaskpassbase64encBHbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tabledeldirdigestdotCall64dplyrdqrngevaluatefansifarverfastmapfitdistrplusFNNfontawesomefsfuturefuture.applygenericsggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppProgressRcppTOMLreshape2reticulaterlangrmarkdownROCRrprojrootRSpectraRtsnesassscalesscattermoresctransformSeuratObjectshinysitmosourcetoolsspspamspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.utilsstringistringrsurvivalsystensortibbletidyrtidyselecttinytexutf8uwotvctrsviridisLitewithrxfunxtableyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Seurat: Tools for Single Cell GenomicsSeurat-package Seurat
Add Azimuth ResultsAddAzimuthResults
Add Azimuth ScoresAddAzimuthScores
Calculate module scores for feature expression programs in single cellsAddModuleScore
Aggregated feature expression by identity classAggregateExpression
The AnchorSet ClassAnchorSet AnchorSet-class
Add info to anchor matrixAnnotateAnchors AnnotateAnchors.default AnnotateAnchors.IntegrationAnchorSet AnnotateAnchors.TransferAnchorSet
Convert objects to CellDataSet objectsas.CellDataSet as.CellDataSet.Seurat
Convert objects to 'Seurat' objectsas.Seurat.CellDataSet as.Seurat.SingleCellExperiment
Convert objects to SingleCellExperiment objectsas.SingleCellExperiment as.SingleCellExperiment.Seurat
Cast to Sparseas.data.frame.Matrix as.sparse.H5Group
The Assay ClassAssay-class
Augments ggplot2-based plot with a PNG image.AugmentPlot
Automagically calculate a point size for ggplot2-based scatter plotsAutoPointSize
Averaged feature expression by identity classAverageExpression
Plot the Barcode Distribution and Calculated Inflection PointsBarcodeInflectionsPlot
Determine text color based on background colorBGTextColor
Create a custom color paletteBlackAndWhite BlueAndRed CustomPalette PurpleAndYellow
Phylogenetic Analysis of Identity ClassesBuildClusterTree
Calculate a perturbation SignatureCalcPerturbSig
Calculate the Barcode Distribution InflectionCalculateBarcodeInflections
Match the case of character vectorsCaseMatch
Cell cycle genescc.genes
Cell cycle genes: 2019 updatecc.genes.updated.2019
Score cell cycle phasesCellCycleScoring
Get Cell NamesCells.SCTModel Cells.SlideSeq Cells.STARmap Cells.VisiumV1
Get a vector of cell names associated with an image (or set of images)CellsByImage
Cell-cell scatter plotCellPlot CellScatter
Cell SelectorCellSelector FeatureLocator
Move outliers towards center on dimension reduction plotCollapseEmbeddingOutliers
Slim down a multi-species expression matrix, when only one species is primarily of interenst.CollapseSpeciesExpressionMatrix
Color dimensional reduction plot by tree splitColorDimSplit
Combine ggplot2-based plots into a single plotCombinePlots
Get the intensity and/or luminance of a colorcontrast-theory Intensity Luminance
Create a SCT Assay objectCreateSCTAssayObject
Run a custom distance function on an input data matrixCustomDistance
DE and EnrichR pathway visualization barplotDEenrichRPlot
Slim down a Seurat objectDietSeurat
Dimensional reduction heatmapDimHeatmap PCHeatmap
Dimensional reduction plotDimPlot ICAPlot PCAPlot TSNEPlot UMAPPlot
The DimReduc ClassDimReduc-class
Discrete colour palettes from palsDiscretePalette
Feature expression heatmapDoHeatmap
Dot plot visualizationDotPlot SplitDotPlotGG
Quickly Pick Relevant DimensionsElbowPlot
Calculate the mean of logged valuesExpMean
Calculate the standard deviation of logged valuesExpSD
Calculate the variance of logged valuesExpVar
Scale and/or center matrix rowwiseFastRowScale
Visualize 'features' on a dimensional reduction plotFeatureHeatmap FeaturePlot
Scatter plot of single cell dataFeatureScatter GenePlot
Filter stray beads from Slide-seq puckFilterSlideSeq
Gene expression markers for all identity classesFindAllMarkers FindAllMarkersNode
Cluster DeterminationFindClusters FindClusters.default FindClusters.Seurat
Finds markers that are conserved between the groupsFindConservedMarkers
Find integration anchorsFindIntegrationAnchors
Gene expression markers of identity classesFindMarkers FindMarkers.Assay FindMarkers.default FindMarkers.DimReduc FindMarkers.SCTAssay FindMarkers.Seurat FindMarkersNode
Construct weighted nearest neighbor graphFindMultiModalNeighbors
(Shared) Nearest-neighbor graph constructionFindNeighbors FindNeighbors.Assay FindNeighbors.default FindNeighbors.dist FindNeighbors.Seurat
Find spatially variable featuresFindSpatiallyVariableFeatures FindSpatiallyVariableFeatures.Assay FindSpatiallyVariableFeatures.default FindSpatiallyVariableFeatures.Seurat
Find subclusters under one clusterFindSubCluster
Find transfer anchorsFindTransferAnchors
Find variable featuresFindVariableFeatures FindVariableFeatures.Assay FindVariableFeatures.default FindVariableFeatures.SCTAssay FindVariableFeatures.Seurat FindVariableGenes
Fold ChangeFoldChange FoldChange.Assay FoldChange.default FoldChange.DimReduc FoldChange.SCTAssay FoldChange.Seurat
Get an Assay object from a given Seurat object.GetAssay GetAssay.Seurat
Get Image DataGetImage.SlideSeq GetImage.STARmap GetImage.VisiumV1
Get integration dataGetIntegrationData
Calculate pearson residuals of features not in the scale.dataGetResidual
Get Tissue CoordinatesGetTissueCoordinates.SlideSeq GetTissueCoordinates.STARmap GetTissueCoordinates.VisiumV1
Get the predicted identityGetTransferPredictions
The Graph ClassGraph-class
Compute the correlation of features broken down by groups with another covariateGroupCorrelation
Boxplot of correlation of a variable (e.g. number of UMIs) with expression dataGroupCorrelationPlot
Hover LocatorHoverLocator
Demultiplex samples based on data from cell 'hashing'HTODemux
Hashtag oligo heatmapHTOHeatmap
Get Variable Feature InformationHVFInfo.SCTAssay
Visualize features in dimensional reduction space interactivelyIFeaturePlot
Spatial Cluster PlotsImageDimPlot
Spatial Feature PlotsImageFeaturePlot
Integrate dataIntegrateData
Integrate low dimensional embeddingsIntegrateEmbeddings IntegrateEmbeddings.IntegrationAnchorSet IntegrateEmbeddings.TransferAnchorSet
The IntegrationAnchorSet ClassIntegrationAnchorSet IntegrationAnchorSet-class
The IntegrationData ClassIntegrationData IntegrationData-class
Visualize clusters spatially and interactivelyISpatialDimPlot
Visualize features spatially and interactivelyISpatialFeaturePlot
Determine statistical significance of PCA scores.JackStraw
The JackStrawData ClassJackStrawData-class
JackStraw PlotJackStrawPlot
L2-Normalize CCAL2CCA
L2-normalizationL2Dim
Label clusters on a ggplot2-based scatter plotLabelClusters
Add text labels to a ggplot2 plotLabeler LabelPoints
Visualize spatial and clustering (dimensional reduction) data in a linked, interactive frameworkLinkedDimPlot LinkedFeaturePlot LinkedPlot LinkedPlots
Load a 10x Genomics Visium Spatial Experiment into a 'Seurat' objectLoad10X_Spatial
Load the Annoy index fileLoadAnnoyIndex
Load Curio Seeker dataLoadCurioSeeker
Load STARmap dataLoadSTARmap
Read and Load 10x Genomics Xenium in-situ dataLoadXenium ReadXenium
Calculate the local structure preservation metricLocalStruct
Normalize raw dataLogNormalize
Calculate the variance to mean ratio of logged valuesLogVMR
Metric for evaluating mapping successMappingScore MappingScore.AnchorSet MappingScore.default
Map query cells to a referenceMapQuery
Merge SCTAssay objectsmerge.SCTAssay
Aggregate expression of multiple features into a single featureMetaFeature
Apply a ceiling and floor to all values in a matrixMinMax
Calculates a mixing metricMixingMetric
Differential expression heatmap for mixscapeMixscapeHeatmap
Linear discriminant analysis on pooled CRISPR screen data.MixscapeLDA
The ModalityWeights ClassModalityWeights ModalityWeights-class
Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)MULTIseqDemux
The Neighbor ClassNeighbor-class
Highlight Neighbors in DimPlotNNPlot
Normalize DataNormalizeData NormalizeData.Assay NormalizeData.default NormalizeData.Seurat
Significant genes from a PCAPCASigGenes
Calculate the percentage of a vector above some thresholdPercentAbove
Calculate the percentage of all counts that belong to a given set of featuresPercentageFeatureSet
Plot clusters as a treePlotClusterTree
Function to plot perturbation score distributions.PlotPerturbScore
Polygon DimPlotPolyDimPlot
Polygon FeaturePlotPolyFeaturePlot
Predict value from nearest neighborsPredictAssay
Function to prepare data for Linear Discriminant Analysis.PrepLDA
Prepare object to run differential expression on SCT assay with multiple modelsPrepSCTFindMarkers
Prepare an object list normalized with sctransform for integration.PrepSCTIntegration
Project Dimensional reduction onto full datasetProjectDim
Project query into UMAP coordinates of a referenceProjectUMAP ProjectUMAP.default ProjectUMAP.DimReduc ProjectUMAP.Seurat
Get Spot RadiusRadius.SlideSeq Radius.STARmap Radius.VisiumV1
Load in data from 10XRead10X
Read 10X hdf5 fileRead10X_h5
Load a 10X Genomics Visium ImageRead10X_Image
Read10x Probe MetadataRead10X_probe_metadata
Read and Load Akoya CODEX dataLoadAkoya ReadAkoya
Load in data from remote or local mtx filesReadMtx
Read and Load Nanostring SMI dataLoadNanostring ReadNanostring
Read output from Parse BiosciencesReadParseBio
Load Slide-seq spatial dataReadSlideSeq
Read output from STARsoloReadSTARsolo
Read Data From VitessceLoadHuBMAPCODEX ReadVitessce
Read and Load MERFISH Input from VizgenLoadVizgen ReadVizgen
Regroup idents based on meta.data infoRegroupIdents
Normalize raw data to fractionsRelativeCounts
Rename Cells in an ObjectRenameCells.SCTAssay RenameCells.SlideSeq RenameCells.STARmap RenameCells.VisiumV1
Single cell ridge plotRidgePlot
Perform Canonical Correlation AnalysisRunCCA RunCCA.default RunCCA.Seurat
Run Independent Component Analysis on gene expressionRunICA RunICA.Assay RunICA.default RunICA.Seurat
Run Linear Discriminant AnalysisRunLDA RunLDA.Assay RunLDA.default RunLDA.Seurat
Run the mark variogram computation on a given position matrix and expression matrix.RunMarkVario
Run MixscapeRunMixscape
Compute Moran's I value.RunMoransI
Run Principal Component AnalysisRunPCA RunPCA.Assay RunPCA.default RunPCA.Seurat
Run Supervised Latent Semantic IndexingRunSLSI RunSLSI.Assay RunSLSI.default RunSLSI.Seurat
Run Supervised Principal Component AnalysisRunSPCA RunSPCA.Assay RunSPCA.default RunSPCA.Seurat
Run t-distributed Stochastic Neighbor EmbeddingRunTSNE RunTSNE.DimReduc RunTSNE.dist RunTSNE.matrix RunTSNE.Seurat
Run UMAPRunUMAP RunUMAP.default RunUMAP.Graph RunUMAP.Neighbor RunUMAP.Seurat
Sample UMISampleUMI
Save the Annoy indexSaveAnnoyIndex
Scale and center the data.ScaleData ScaleData.Assay ScaleData.default ScaleData.Seurat
Get image scale factorsScaleFactors scalefactors ScaleFactors.VisiumV1
Compute Jackstraw scores significance.ScoreJackStraw ScoreJackStraw.DimReduc ScoreJackStraw.JackStrawData ScoreJackStraw.Seurat
The SCTModel Classlevels.SCTAssay levels<-.SCTAssay SCTAssay SCTAssay-class SCTModel
Use regularized negative binomial regression to normalize UMI count dataSCTransform
Get SCT results from an AssaySCTResults SCTResults.SCTAssay SCTResults.SCTModel SCTResults.Seurat SCTResults<- SCTResults<-.SCTAssay SCTResults<-.SCTModel
Select integration featuresSelectIntegrationFeatures
Set integration dataSetIntegrationData
Find the Quantile of DataSetQuantile
The Seurat ClassSeurat-class
The SeuratCommand ClassSeuratCommand-class
Seurat ThemesBoldTitle CenterTitle DarkTheme FontSize NoAxes NoGrid NoLegend RestoreLegend RotatedAxis SeuratAxes SeuratTheme SpatialTheme WhiteBackground
The SlideSeq classSlideSeq SlideSeq-class
The SpatialImage ClassSpatialImage-class
Visualize spatial clustering and expression data.SpatialDimPlot SpatialFeaturePlot SpatialPlot
Splits object into a list of subsetted objects.SplitObject
The STARmap classSTARmap STARmap-class
Subset an AnchorSet objectsubset.AnchorSet
Subset a Seurat Object based on the Barcode Distribution Inflection PointsSubsetByBarcodeInflections
Find cells with highest scores for a given dimensional reduction techniqueTopCells
Find features with highest scores for a given dimensional reduction techniqueTopFeatures
Get nearest neighbors for given cellTopNeighbors
The TransferAnchorSet ClassTransferAnchorSet TransferAnchorSet-class
Transfer dataTransferData
Update pre-V4 Assays generated with SCTransform in the Seurat to the new SCTAssay classUpdateSCTAssays
Get updated synonyms for gene symbolsGeneSymbolThesarus UpdateSymbolList
View variable featuresMeanVarPlot VariableFeaturePlot VariableGenePlot
The VisiumV1 classVisiumV1 VisiumV1-class
Visualize Dimensional Reduction genesVizDimLoadings
Single cell violin plotVlnPlot