# Tools for Single Cell Genomics

## Documentation for package ‘Seurat’ version 5.5.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J L M N P R S T U V W

Seurat-package | Seurat: Tools for Single Cell Genomics

## -- A --

AddAzimuthResults | Add Azimuth Results
AddModuleScore | Calculate module scores for feature expression programs in single cells
AddModuleScore.Assay | Calculate module scores for feature expression programs in single cells
AddModuleScore.Seurat | Calculate module scores for feature expression programs in single cells
AddModuleScore.StdAssay | 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 | Get the Pearson residuals from an sctransform-normalized dataset.
FetchResiduals.SCTAssay | Get the Pearson residuals from an sctransform-normalized dataset.
FetchResiduals.Seurat | Get the Pearson residuals from an sctransform-normalized dataset.
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
Format10X_GeoJson_CellID | Format 10X Genomics GeoJson cell IDs

## -- 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
GetImage.VisiumV2 | 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
InteractiveSpatialPlot | Interactive Spatial Cell Selection Tool
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_HD_GeoJson | Load 10X Genomics GeoJson
Read10X_Image | Load a 10X Genomics Visium Image
Read10X_probe_metadata | Read10x Probe Metadata
Read10X_ScaleFactors | Load 10X Genomics Visium Scale Factors
Read10X_Segmentations | Load 10X Genomics Visium Cell Segmentations
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
RunICA.StdAssay | 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
RunLeiden | Run Leiden clustering algorithm
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
RunSLSI.StdAssay | 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.SlideSeq | Get image scale factors
ScaleFactors.STARmap | 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