AddAzimuthResults       Add Azimuth Results
AddModuleScore          Calculate module scores for feature expression
                        programs in single cells
AggregateExpression     Aggregated feature expression by identity class
AnchorSet-class         The AnchorSet Class
AnnotateAnchors         Add info to anchor matrix
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
BGTextColor             Determine text color based on background color
BarcodeInflectionsPlot
                        Plot the Barcode Distribution and Calculated
                        Inflection Points
BlackAndWhite           Create a custom color palette
BridgeCellsRepresentation
                        Construct a dictionary representation for each
                        unimodal dataset
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
CCAIntegration          Seurat-CCA Integration
CalcPerturbSig          Calculate a perturbation Signature
CalculateBarcodeInflections
                        Calculate the Barcode Distribution Inflection
CaseMatch               Match the case of character vectors
CellCycleScoring        Score cell cycle phases
CellScatter             Cell-cell scatter plot
CellSelector            Cell Selector
Cells.SCTModel          Get Cell Names
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
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
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
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
FastRPCAIntegration     Perform integration on the joint PCA cell
                        embeddings.
FastRowScale            Scale and/or center matrix rowwise
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.
FilterSlideSeq          Filter stray beads from Slide-seq puck
FindAllMarkers          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
FindConservedMarkers    Finds markers that are conserved between the
                        groups
FindIntegrationAnchors
                        Find integration anchors
FindMarkers             Gene expression markers of identity classes
FindMultiModalNeighbors
                        Construct weighted nearest neighbor graph
FindNeighbors           (Shared) Nearest-neighbor graph construction
FindSpatiallyVariableFeatures
                        Find spatially variable features
FindSubCluster          Find subclusters under one cluster
FindTransferAnchors     Find transfer anchors
FindVariableFeatures    Find variable features
FoldChange              Fold Change
Format10X_GeoJson_CellID
                        Format 10X Genomics GeoJson cell IDs
GetAssay                Get an Assay object from a given Seurat object.
GetImage.SlideSeq       Get Image Data
GetIntegrationData      Get integration data
GetResidual             Calculate pearson residuals of features not in
                        the scale.data
GetTissueCoordinates.SlideSeq
                        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
HTODemux                Demultiplex samples based on data from cell
                        'hashing'
HTOHeatmap              Hashtag oligo heatmap
HVFInfo.SCTAssay        Get Variable Feature Information
HarmonyIntegration      Harmony Integration
HoverLocator            Hover Locator
IFeaturePlot            Visualize features in dimensional reduction
                        space interactively
ISpatialDimPlot         Visualize clusters spatially and interactively
ISpatialFeaturePlot     Visualize features spatially and interactively
ImageDimPlot            Spatial Cluster Plots
ImageFeaturePlot        Spatial Feature Plots
IntegrateData           Integrate data
IntegrateEmbeddings     Integrate low dimensional embeddings
IntegrateLayers         Integrate Layers
IntegrationAnchorSet-class
                        The IntegrationAnchorSet Class
IntegrationData-class   The IntegrationData Class
InteractiveSpatialPlot
                        Interactive Spatial Cell Selection Tool
JackStraw               Determine statistical significance of PCA
                        scores.
JackStrawData-class     The JackStrawData Class
JackStrawPlot           JackStraw Plot
JointPCAIntegration     Seurat-Joint PCA Integration
L2CCA                   L2-Normalize CCA
L2Dim                   L2-normalization
LabelClusters           Label clusters on a ggplot2-based scatter plot
LabelPoints             Add text labels to a ggplot2 plot
LeverageScore           Leverage Score Calculation
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
LoadAnnoyIndex          Load the Annoy index file
LoadCurioSeeker         Load Curio Seeker data
LoadSTARmap             Load STARmap data
LoadXenium              Read and Load 10x Genomics Xenium in-situ data
LocalStruct             Calculate the local structure preservation
                        metric
LogNormalize            Normalize Raw Data
LogVMR                  Calculate the variance to mean ratio of logged
                        values
MULTIseqDemux           Demultiplex samples based on classification
                        method from MULTI-seq (McGinnis et al., bioRxiv
                        2018)
MapQuery                Map query cells to a reference
MappingScore            Metric for evaluating mapping success
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-class   The ModalityWeights Class
NNPlot                  Highlight Neighbors in DimPlot
NNtoGraph               Convert Neighbor class to an asymmetrical Graph
                        class
Neighbor-class          The Neighbor Class
NormalizeData           Normalize Data
PCASigGenes             Significant genes from a PCA
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
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.
PrepareBridgeReference
                        Prepare the bridge and reference datasets
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
PseudobulkExpression    Pseudobulk Expression
RPCAIntegration         Seurat-RPCA Integration
Radius.SlideSeq         Get Spot Radius
Read10X                 Load in data from 10X
Read10X_Coordinates     Load 10X Genomics Visium Tissue Positions
Read10X_HD_GeoJson      Load 10X Genomics GeoJson
Read10X_Image           Load a 10X Genomics Visium Image
Read10X_ScaleFactors    Load 10X Genomics Visium Scale Factors
Read10X_Segmentations   Load 10X Genomics Visium Cell Segmentations
Read10X_h5              Read 10X hdf5 file
Read10X_probe_metadata
                        Read10x Probe Metadata
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
ReadSTARsolo            Read output from STARsolo
ReadSlideSeq            Load Slide-seq spatial data
ReadVitessce            Read Data From Vitessce
ReadVizgen              Read and Load MERFISH Input from Vizgen
RegroupIdents           Regroup idents based on meta.data info
RelativeCounts          Normalize raw data to fractions
RenameCells.SCTAssay    Rename Cells in an Object
RidgePlot               Single cell ridge plot
RunCCA                  Perform Canonical Correlation Analysis
RunGraphLaplacian       Run Graph Laplacian Eigendecomposition
RunICA                  Run Independent Component Analysis on gene
                        expression
RunLDA                  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
RunSLSI                 Run Supervised Latent Semantic Indexing
RunSPCA                 Run Supervised Principal Component Analysis
RunTSNE                 Run t-distributed Stochastic Neighbor Embedding
RunUMAP                 Run UMAP
SCTAssay-class          The SCTModel Class
SCTResults              Get SCT results from an Assay
SCTransform             Perform sctransform-based normalization
STARmap-class           The STARmap class
SampleUMI               Sample UMI
SaveAnnoyIndex          Save the Annoy index
ScaleData               Scale and center the data.
ScaleFactors            Get image scale factors
ScoreJackStraw          Compute Jackstraw scores significance.
SelectIntegrationFeatures
                        Select integration features
SelectIntegrationFeatures5
                        Select integration features
SelectSCTIntegrationFeatures
                        Select SCT integration features
SetIntegrationData      Set integration data
SetQuantile             Find the Quantile of Data
Seurat-class            The Seurat Class
Seurat-package          Seurat: Tools for Single Cell Genomics
SeuratCommand-class     The SeuratCommand Class
SeuratTheme             Seurat Themes
SketchData              Sketch Data
SlideSeq-class          The SlideSeq class
SpatialImage-class      The SpatialImage Class
SpatialPlot             Visualize spatial clustering and expression
                        data.
SplitObject             Splits object into a list of subsetted objects.
SubsetByBarcodeInflections
                        Subset a Seurat Object based on the Barcode
                        Distribution Inflection Points
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-class
                        The TransferAnchorSet Class
TransferData            Transfer data
TransferSketchLabels    Transfer data from sketch data to full data
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
VariableFeaturePlot     View variable features
VisiumV1-class          The VisiumV1 class
VisiumV2-class          The VisiumV2 class
VizDimLoadings          Visualize Dimensional Reduction genes
VlnPlot                 Single cell violin plot
as.CellDataSet          Convert objects to CellDataSet objects
as.Seurat.CellDataSet   Convert objects to 'Seurat' objects
as.SingleCellExperiment
                        Convert objects to SingleCellExperiment objects
as.sparse.H5Group       Cast to Sparse
cc.genes                Cell cycle genes
cc.genes.updated.2019   Cell cycle genes: 2019 update
contrast-theory         Get the intensity and/or luminance of a color
merge.SCTAssay          Merge SCTAssay objects
subset.AnchorSet        Subset an AnchorSet object
