Tools for Single Cell Genomics

Documentation for package ‘Seurat’ version 5.1.0

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Seurat: Tools for Single Cell Genomics

-- A --

AddAzimuthResults	Add Azimuth Results
AddModuleScore	Calculate module scores for feature expression programs in single cells
AggregateExpression	Aggregated feature expression by identity class
AnchorSet	The AnchorSet Class
AnchorSet-class	The AnchorSet Class
AnnotateAnchors	Add info to anchor matrix
AnnotateAnchors.default	Add info to anchor matrix
AnnotateAnchors.IntegrationAnchorSet	Add info to anchor matrix
AnnotateAnchors.TransferAnchorSet	Add info to anchor matrix
as.CellDataSet	Convert objects to CellDataSet objects
as.CellDataSet.Seurat	Convert objects to CellDataSet objects
as.data.frame.Matrix	Cast to Sparse
as.Seurat.CellDataSet	Convert objects to 'Seurat' objects
as.Seurat.SingleCellExperiment	Convert objects to 'Seurat' objects
as.SingleCellExperiment	Convert objects to SingleCellExperiment objects
as.SingleCellExperiment.Seurat	Convert objects to SingleCellExperiment objects
as.sparse.H5Group	Cast to Sparse
Assay-class	The Assay Class
AugmentPlot	Augments ggplot2-based plot with a PNG image.
AutoPointSize	Automagically calculate a point size for ggplot2-based scatter plots
AverageExpression	Averaged feature expression by identity class

-- B --

BarcodeInflectionsPlot	Plot the Barcode Distribution and Calculated Inflection Points
BGTextColor	Determine text color based on background color
BlackAndWhite	Create a custom color palette
BlueAndRed	Create a custom color palette
BoldTitle	Seurat Themes
BridgeCellsRepresentation	Construct a dictionary representation for each unimodal dataset
BridgeReferenceSet	The BridgeReferenceSet Class The BridgeReferenceSet is an output from PrepareBridgeReference
BridgeReferenceSet-class	The BridgeReferenceSet Class The BridgeReferenceSet is an output from PrepareBridgeReference
BuildClusterTree	Phylogenetic Analysis of Identity Classes
BuildNicheAssay	Construct an assay for spatial niche analysis

-- C --

CalcPerturbSig	Calculate a perturbation Signature
CalculateBarcodeInflections	Calculate the Barcode Distribution Inflection
CaseMatch	Match the case of character vectors
cc.genes	Cell cycle genes
cc.genes.updated.2019	Cell cycle genes: 2019 update
CCAIntegration	Seurat-CCA Integration
CellCycleScoring	Score cell cycle phases
CellPlot	Cell-cell scatter plot
Cells.SCTModel	Get Cell Names
Cells.SlideSeq	Get Cell Names
Cells.STARmap	Get Cell Names
Cells.VisiumV1	Get Cell Names
CellScatter	Cell-cell scatter plot
CellSelector	Cell Selector
CenterTitle	Seurat Themes
CollapseEmbeddingOutliers	Move outliers towards center on dimension reduction plot
CollapseSpeciesExpressionMatrix	Slim down a multi-species expression matrix, when only one species is primarily of interenst.
ColorDimSplit	Color dimensional reduction plot by tree split
CombinePlots	Combine ggplot2-based plots into a single plot
contrast-theory	Get the intensity and/or luminance of a color
CreateCategoryMatrix	Create one hot matrix for a given label
CreateSCTAssayObject	Create a SCT Assay object
CustomDistance	Run a custom distance function on an input data matrix
CustomPalette	Create a custom color palette

-- D --

DarkTheme	Seurat Themes
DEenrichRPlot	DE and EnrichR pathway visualization barplot
DietSeurat	Slim down a Seurat object
DimHeatmap	Dimensional reduction heatmap
DimPlot	Dimensional reduction plot
DimReduc-class	The DimReduc Class
DiscretePalette	Discrete colour palettes from pals
DoHeatmap	Feature expression heatmap
DotPlot	Dot plot visualization

-- E --

ElbowPlot	Quickly Pick Relevant Dimensions
ExpMean	Calculate the mean of logged values
ExpSD	Calculate the standard deviation of logged values
ExpVar	Calculate the variance of logged values

-- F --

FastRowScale	Scale and/or center matrix rowwise
FastRPCAIntegration	Perform integration on the joint PCA cell embeddings.
FeatureHeatmap	Visualize 'features' on a dimensional reduction plot
FeatureLocator	Cell Selector
FeaturePlot	Visualize 'features' on a dimensional reduction plot
FeatureScatter	Scatter plot of single cell data
FetchResiduals	Calculate pearson residuals of features not in the scale.data
FilterSlideSeq	Filter stray beads from Slide-seq puck
FindAllMarkers	Gene expression markers for all identity classes
FindAllMarkersNode	Gene expression markers for all identity classes
FindBridgeIntegrationAnchors	Find integration bridge anchors between query and extended bridge-reference
FindBridgeTransferAnchors	Find bridge anchors between query and extended bridge-reference
FindClusters	Cluster Determination
FindClusters.default	Cluster Determination
FindClusters.Seurat	Cluster Determination
FindConservedMarkers	Finds markers that are conserved between the groups
FindIntegrationAnchors	Find integration anchors
FindMarkers	Gene expression markers of identity classes
FindMarkers.Assay	Gene expression markers of identity classes
FindMarkers.default	Gene expression markers of identity classes
FindMarkers.DimReduc	Gene expression markers of identity classes
FindMarkers.SCTAssay	Gene expression markers of identity classes
FindMarkers.Seurat	Gene expression markers of identity classes
FindMarkersNode	Gene expression markers of identity classes
FindMultiModalNeighbors	Construct weighted nearest neighbor graph
FindNeighbors	(Shared) Nearest-neighbor graph construction
FindNeighbors.Assay	(Shared) Nearest-neighbor graph construction
FindNeighbors.default	(Shared) Nearest-neighbor graph construction
FindNeighbors.dist	(Shared) Nearest-neighbor graph construction
FindNeighbors.Seurat	(Shared) Nearest-neighbor graph construction
FindSpatiallyVariableFeatures	Find spatially variable features
FindSpatiallyVariableFeatures.Assay	Find spatially variable features
FindSpatiallyVariableFeatures.default	Find spatially variable features
FindSpatiallyVariableFeatures.Seurat	Find spatially variable features
FindSpatiallyVariableFeatures.StdAssay	Find spatially variable features
FindSubCluster	Find subclusters under one cluster
FindTransferAnchors	Find transfer anchors
FindVariableFeatures	Find variable features
FindVariableFeatures.Assay	Find variable features
FindVariableFeatures.SCTAssay	Find variable features
FindVariableFeatures.Seurat	Find variable features
FindVariableFeatures.V3Matrix	Find variable features
FindVariableGenes	Find variable features
FoldChange	Fold Change
FoldChange.Assay	Fold Change
FoldChange.default	Fold Change
FoldChange.DimReduc	Fold Change
FoldChange.SCTAssay	Fold Change
FoldChange.Seurat	Fold Change
FontSize	Seurat Themes

-- G --

GenePlot	Scatter plot of single cell data
GeneSymbolThesarus	Get updated synonyms for gene symbols
GetAssay	Get an Assay object from a given Seurat object.
GetAssay.Seurat	Get an Assay object from a given Seurat object.
GetImage.SlideSeq	Get Image Data
GetImage.STARmap	Get Image Data
GetImage.VisiumV1	Get Image Data
GetIntegrationData	Get integration data
GetResidual	Calculate pearson residuals of features not in the scale.data
GetTissueCoordinates.SlideSeq	Get Tissue Coordinates
GetTissueCoordinates.STARmap	Get Tissue Coordinates
GetTissueCoordinates.VisiumV1	Get Tissue Coordinates
GetTissueCoordinates.VisiumV2	Get Tissue Coordinates
GetTransferPredictions	Get the predicted identity
Graph-class	The Graph Class
GroupCorrelation	Compute the correlation of features broken down by groups with another covariate
GroupCorrelationPlot	Boxplot of correlation of a variable (e.g. number of UMIs) with expression data

-- H --

HarmonyIntegration	Harmony Integration
HoverLocator	Hover Locator
HTODemux	Demultiplex samples based on data from cell 'hashing'
HTOHeatmap	Hashtag oligo heatmap
HVFInfo.SCTAssay	Get Variable Feature Information

-- I --

ICAPlot	Dimensional reduction plot
IFeaturePlot	Visualize features in dimensional reduction space interactively
ImageDimPlot	Spatial Cluster Plots
ImageFeaturePlot	Spatial Feature Plots
IntegrateData	Integrate data
IntegrateEmbeddings	Integrate low dimensional embeddings
IntegrateEmbeddings.IntegrationAnchorSet	Integrate low dimensional embeddings
IntegrateEmbeddings.TransferAnchorSet	Integrate low dimensional embeddings
IntegrateLayers	Integrate Layers
IntegrationAnchorSet	The IntegrationAnchorSet Class
IntegrationAnchorSet-class	The IntegrationAnchorSet Class
IntegrationData	The IntegrationData Class
IntegrationData-class	The IntegrationData Class
Intensity	Get the intensity and/or luminance of a color
ISpatialDimPlot	Visualize clusters spatially and interactively
ISpatialFeaturePlot	Visualize features spatially and interactively

-- J --

JackStraw	Determine statistical significance of PCA scores.
JackStrawData-class	The JackStrawData Class
JackStrawPlot	JackStraw Plot
JointPCAIntegration	Seurat-Joint PCA Integration

-- L --

L2CCA	L2-Normalize CCA
L2Dim	L2-normalization
LabelClusters	Label clusters on a ggplot2-based scatter plot
Labeler	Add text labels to a ggplot2 plot
LabelPoints	Add text labels to a ggplot2 plot
levels.SCTAssay	The SCTModel Class
levels<-.SCTAssay	The SCTModel Class
LeverageScore	Leverage Score Calculation
LeverageScore.Assay	Leverage Score Calculation
LeverageScore.default	Leverage Score Calculation
LeverageScore.Seurat	Leverage Score Calculation
LeverageScore.StdAssay	Leverage Score Calculation
LinkedDimPlot	Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework
LinkedFeaturePlot	Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework
LinkedPlot	Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework
LinkedPlots	Visualize spatial and clustering (dimensional reduction) data in a linked, interactive framework
Load10X_Spatial	Load a 10x Genomics Visium Spatial Experiment into a 'Seurat' object
LoadAkoya	Read and Load Akoya CODEX data
LoadAnnoyIndex	Load the Annoy index file
LoadCurioSeeker	Load Curio Seeker data
LoadHuBMAPCODEX	Read Data From Vitessce
LoadNanostring	Read and Load Nanostring SMI data
LoadSTARmap	Load STARmap data
LoadVizgen	Read and Load MERFISH Input from Vizgen
LoadXenium	Read and Load 10x Genomics Xenium in-situ data
LocalStruct	Calculate the local structure preservation metric
LogNormalize	Normalize Raw Data
LogNormalize.data.frame	Normalize Raw Data
LogNormalize.default	Normalize Raw Data
LogNormalize.V3Matrix	Normalize Raw Data
LogVMR	Calculate the variance to mean ratio of logged values
Luminance	Get the intensity and/or luminance of a color

-- M --

MappingScore	Metric for evaluating mapping success
MappingScore.AnchorSet	Metric for evaluating mapping success
MappingScore.default	Metric for evaluating mapping success
MapQuery	Map query cells to a reference
MeanVarPlot	View variable features
merge.SCTAssay	Merge SCTAssay objects
MetaFeature	Aggregate expression of multiple features into a single feature
MinMax	Apply a ceiling and floor to all values in a matrix
MixingMetric	Calculates a mixing metric
MixscapeHeatmap	Differential expression heatmap for mixscape
MixscapeLDA	Linear discriminant analysis on pooled CRISPR screen data.
ModalityWeights	The ModalityWeights Class
ModalityWeights-class	The ModalityWeights Class
MULTIseqDemux	Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)

-- N --

Neighbor-class	The Neighbor Class
NNPlot	Highlight Neighbors in DimPlot
NNtoGraph	Convert Neighbor class to an asymmetrical Graph class
NoAxes	Seurat Themes
NoGrid	Seurat Themes
NoLegend	Seurat Themes
NormalizeData	Normalize Data
NormalizeData.Assay	Normalize Data
NormalizeData.Seurat	Normalize Data
NormalizeData.V3Matrix	Normalize Data

-- P --

PCAPlot	Dimensional reduction plot
PCASigGenes	Significant genes from a PCA
PCHeatmap	Dimensional reduction heatmap
PercentAbove	Calculate the percentage of a vector above some threshold
PercentageFeatureSet	Calculate the percentage of all counts that belong to a given set of features
PlotClusterTree	Plot clusters as a tree
PlotPerturbScore	Function to plot perturbation score distributions.
PolyDimPlot	Polygon DimPlot
PolyFeaturePlot	Polygon FeaturePlot
PredictAssay	Predict value from nearest neighbors
PrepareBridgeReference	Prepare the bridge and reference datasets
PrepLDA	Function to prepare data for Linear Discriminant Analysis.
PrepSCTFindMarkers	Prepare object to run differential expression on SCT assay with multiple models
PrepSCTIntegration	Prepare an object list normalized with sctransform for integration.
ProjectData	Project full data to the sketch assay
ProjectDim	Project Dimensional reduction onto full dataset
ProjectDimReduc	Project query data to reference dimensional reduction
ProjectIntegration	Integrate embeddings from the integrated sketched.assay
ProjectUMAP	Project query into UMAP coordinates of a reference
ProjectUMAP.default	Project query into UMAP coordinates of a reference
ProjectUMAP.DimReduc	Project query into UMAP coordinates of a reference
ProjectUMAP.Seurat	Project query into UMAP coordinates of a reference
PseudobulkExpression	Pseudobulk Expression
PseudobulkExpression.Assay	Pseudobulk Expression
PseudobulkExpression.Seurat	Pseudobulk Expression
PseudobulkExpression.StdAssay	Pseudobulk Expression
PurpleAndYellow	Create a custom color palette

-- R --

Radius.SlideSeq	Get Spot Radius
Radius.STARmap	Get Spot Radius
Radius.VisiumV1	Get Spot Radius
Radius.VisiumV2	Get Spot Radius
Read10X	Load in data from 10X
Read10X_Coordinates	Load 10X Genomics Visium Tissue Positions
Read10X_h5	Read 10X hdf5 file
Read10X_Image	Load a 10X Genomics Visium Image
Read10X_probe_metadata	Read10x Probe Metadata
Read10X_ScaleFactors	Load 10X Genomics Visium Scale Factors
ReadAkoya	Read and Load Akoya CODEX data
ReadMtx	Load in data from remote or local mtx files
ReadNanostring	Read and Load Nanostring SMI data
ReadParseBio	Read output from Parse Biosciences
ReadSlideSeq	Load Slide-seq spatial data
ReadSTARsolo	Read output from STARsolo
ReadVitessce	Read Data From Vitessce
ReadVizgen	Read and Load MERFISH Input from Vizgen
ReadXenium	Read and Load 10x Genomics Xenium in-situ data
RegroupIdents	Regroup idents based on meta.data info
RelativeCounts	Normalize raw data to fractions
RenameCells.SCTAssay	Rename Cells in an Object
RenameCells.SlideSeq	Rename Cells in an Object
RenameCells.STARmap	Rename Cells in an Object
RenameCells.VisiumV1	Rename Cells in an Object
RestoreLegend	Seurat Themes
RidgePlot	Single cell ridge plot
RotatedAxis	Seurat Themes
RPCAIntegration	Seurat-RPCA Integration
RunCCA	Perform Canonical Correlation Analysis
RunCCA.default	Perform Canonical Correlation Analysis
RunCCA.Seurat	Perform Canonical Correlation Analysis
RunGraphLaplacian	Run Graph Laplacian Eigendecomposition
RunGraphLaplacian.default	Run Graph Laplacian Eigendecomposition
RunGraphLaplacian.Seurat	Run Graph Laplacian Eigendecomposition
RunICA	Run Independent Component Analysis on gene expression
RunICA.Assay	Run Independent Component Analysis on gene expression
RunICA.default	Run Independent Component Analysis on gene expression
RunICA.Seurat	Run Independent Component Analysis on gene expression
RunLDA	Run Linear Discriminant Analysis
RunLDA.Assay	Run Linear Discriminant Analysis
RunLDA.default	Run Linear Discriminant Analysis
RunLDA.Seurat	Run Linear Discriminant Analysis
RunMarkVario	Run the mark variogram computation on a given position matrix and expression matrix.
RunMixscape	Run Mixscape
RunMoransI	Compute Moran's I value.
RunPCA	Run Principal Component Analysis
RunPCA.Assay	Run Principal Component Analysis
RunPCA.default	Run Principal Component Analysis
RunPCA.Seurat	Run Principal Component Analysis
RunSLSI	Run Supervised Latent Semantic Indexing
RunSLSI.Assay	Run Supervised Latent Semantic Indexing
RunSLSI.default	Run Supervised Latent Semantic Indexing
RunSLSI.Seurat	Run Supervised Latent Semantic Indexing
RunSPCA	Run Supervised Principal Component Analysis
RunSPCA.Assay	Run Supervised Principal Component Analysis
RunSPCA.Assay5	Run Supervised Principal Component Analysis
RunSPCA.default	Run Supervised Principal Component Analysis
RunSPCA.Seurat	Run Supervised Principal Component Analysis
RunTSNE	Run t-distributed Stochastic Neighbor Embedding
RunTSNE.DimReduc	Run t-distributed Stochastic Neighbor Embedding
RunTSNE.dist	Run t-distributed Stochastic Neighbor Embedding
RunTSNE.matrix	Run t-distributed Stochastic Neighbor Embedding
RunTSNE.Seurat	Run t-distributed Stochastic Neighbor Embedding
RunUMAP	Run UMAP
RunUMAP.default	Run UMAP
RunUMAP.Graph	Run UMAP
RunUMAP.Neighbor	Run UMAP
RunUMAP.Seurat	Run UMAP

-- S --

SampleUMI	Sample UMI
SaveAnnoyIndex	Save the Annoy index
ScaleData	Scale and center the data.
ScaleData.Assay	Scale and center the data.
ScaleData.default	Scale and center the data.
ScaleData.IterableMatrix	Scale and center the data.
ScaleData.Seurat	Scale and center the data.
ScaleFactors	Get image scale factors
scalefactors	Get image scale factors
ScaleFactors.VisiumV1	Get image scale factors
ScaleFactors.VisiumV2	Get image scale factors
ScoreJackStraw	Compute Jackstraw scores significance.
ScoreJackStraw.DimReduc	Compute Jackstraw scores significance.
ScoreJackStraw.JackStrawData	Compute Jackstraw scores significance.
ScoreJackStraw.Seurat	Compute Jackstraw scores significance.
SCTAssay	The SCTModel Class
SCTAssay-class	The SCTModel Class
SCTModel	The SCTModel Class
SCTransform	Perform sctransform-based normalization
SCTransform.Assay	Perform sctransform-based normalization
SCTransform.default	Perform sctransform-based normalization
SCTransform.IterableMatrix	Perform sctransform-based normalization
SCTransform.Seurat	Perform sctransform-based normalization
SCTResults	Get SCT results from an Assay
SCTResults.SCTAssay	Get SCT results from an Assay
SCTResults.SCTModel	Get SCT results from an Assay
SCTResults.Seurat	Get SCT results from an Assay
SCTResults<-	Get SCT results from an Assay
SCTResults<-.SCTAssay	Get SCT results from an Assay
SCTResults<-.SCTModel	Get SCT results from an Assay
SelectIntegrationFeatures	Select integration features
SelectIntegrationFeatures5	Select integration features
SelectSCTIntegrationFeatures	Select SCT integration features
SetIntegrationData	Set integration data
SetQuantile	Find the Quantile of Data
Seurat	Seurat: Tools for Single Cell Genomics
Seurat-class	The Seurat Class
SeuratAxes	Seurat Themes
SeuratCommand-class	The SeuratCommand Class
SeuratTheme	Seurat Themes
SketchData	Sketch Data
SlideSeq	The SlideSeq class
SlideSeq-class	The SlideSeq class
SpatialDimPlot	Visualize spatial clustering and expression data.
SpatialFeaturePlot	Visualize spatial clustering and expression data.
SpatialImage-class	The SpatialImage Class
SpatialPlot	Visualize spatial clustering and expression data.
SpatialTheme	Seurat Themes
SplitDotPlotGG	Dot plot visualization
SplitObject	Splits object into a list of subsetted objects.
STARmap	The STARmap class
STARmap-class	The STARmap class
subset.AnchorSet	Subset an AnchorSet object
SubsetByBarcodeInflections	Subset a Seurat Object based on the Barcode Distribution Inflection Points

-- T --

TopCells	Find cells with highest scores for a given dimensional reduction technique
TopFeatures	Find features with highest scores for a given dimensional reduction technique
TopNeighbors	Get nearest neighbors for given cell
TransferAnchorSet	The TransferAnchorSet Class
TransferAnchorSet-class	The TransferAnchorSet Class
TransferData	Transfer data
TransferSketchLabels	Transfer data from sketch data to full data
TSNEPlot	Dimensional reduction plot

-- U --

UMAPPlot	Dimensional reduction plot
UnSketchEmbeddings	Transfer embeddings from sketched cells to the full data
UpdateSCTAssays	Update pre-V4 Assays generated with SCTransform in the Seurat to the new SCTAssay class
UpdateSymbolList	Get updated synonyms for gene symbols

-- V --

VariableFeaturePlot	View variable features
VariableGenePlot	View variable features
VisiumV1	The VisiumV1 class
VisiumV1-class	The VisiumV1 class
VisiumV2	The VisiumV2 class
VisiumV2-class	The VisiumV2 class
VizDimLoadings	Visualize Dimensional Reduction genes
VlnPlot	Single cell violin plot

-- W --

WhiteBackground

Seurat Themes