AddImputedScore         Calculate imputed expression values
AddMetaData             Add Metadata
AddModuleScore          Calculate module scores for gene expression
                        programs in single cells
AddSamples              Add samples into existing Seurat object.
AddSmoothedScore        Calculate smoothed expression values
AlignSubspace           Align subspaces using dynamic time warping
                        (DTW)
AssessNodes             Assess Internal Nodes
AssessSplit             Assess Cluster Split
AugmentPlot             Augments ggplot2 scatterplot with a PNG image.
AverageDetectionRate    Probability of detection by identity class
AverageExpression       Averaged gene expression by identity class
AveragePCA              Average PCA scores by identity class
BatchGene               Identify potential genes associated with batch
                        effects
BlackAndWhite           A black and white color palette
BuildClusterTree        Phylogenetic Analysis of Identity Classes
BuildRFClassifier       Build Random Forest Classifier
BuildSNN                SNN Graph Construction
CalcAlignmentMetric     Calculate an alignment score
CalcVarExpRatio         Calculate the ratio of variance explained by
                        ICA or PCA to CCA
CaseMatch               Match the case of character vectors
CellCycleScoring        Score cell cycle phases
CellPlot                Cell-cell scatter plot
ClassifyCells           Classify New Data
CollapseSpeciesExpressionMatrix
                        Slim down a multi-species expression matrix,
                        when only one species is primarily of
                        interenst.
ColorTSNESplit          Color tSNE Plot Based on Split
CombineIdent            Sets identity class information to be a
                        combination of two object attributes
Convert                 Convert Seurat objects to other classes and
                        vice versa
CreateSeuratObject      Initialize and setup the Seurat object
CustomDistance          Run a custom distance function on an input data
                        matrix
CustomPalette           Create a custom color palette
DBClustDimension        Perform spectral density clustering on single
                        cells
DESeq2DETest            Differential expression using DESeq2
DMEmbed                 Diffusion Maps Cell Embeddings Accessor
                        Function
DMPlot                  Plot Diffusion map
DarkTheme               Dark Theme
DiffExpTest             Likelihood ratio test for zero-inflated data
DiffTTest               Differential expression testing using Student's
                        t-test
DimElbowPlot            Quickly Pick Relevant Dimensions
DimHeatmap              Dimensional reduction heatmap
DimPlot                 Dimensional reduction plot
DimTopCells             Find cells with highest scores for a given
                        dimensional reduction technique
DimTopGenes             Find genes with highest scores for a given
                        dimensional reduction technique
DoHeatmap               Gene expression heatmap
DoKMeans                K-Means Clustering
DotPlot                 Dot plot visualization
DotPlotOld              Old Dot plot visualization (pre-ggplot
                        implementation) Intuitive way of visualizing
                        how gene expression changes across different
                        identity classes (clusters). The size of the
                        dot encodes the percentage of cells within a
                        class, while the color encodes the
                        AverageExpression level of 'expressing' cells
                        (green is high).
ExpMean                 Calculate the mean of logged values
ExpSD                   Calculate the standard deviation of logged
                        values
ExpVar                  Calculate the variance of logged values
ExtractField            Extract delimiter information from a string.
FastWhichCells          FastWhichCells Identify cells matching certain
                        criteria (limited to character values)
FeatureHeatmap          Vizualization of multiple features
FeatureLocator          Feature Locator
FeaturePlot             Visualize 'features' on a dimensional reduction
                        plot
FetchData               Access cellular data
FilterCells             Return a subset of the Seurat object
FindAllMarkers          Gene expression markers for all identity
                        classes
FindAllMarkersNode      Find all markers for a node
FindClusters            Cluster Determination
FindConservedMarkers    Finds markers that are conserved between the
                        two groups
FindGeneTerms           Find gene terms from Enrichr
FindMarkers             Gene expression markers of identity classes
FindMarkersNode         Gene expression markers of identity classes
                        defined by a phylogenetic clade
FindVariableGenes       Identify variable genes
FitGeneK                Build mixture models of gene expression
GenePlot                Scatter plot of single cell data
GenesInCluster          GenesInCluster
GetAssayData            Accessor function for multimodal data
GetCellEmbeddings       Dimensional Reduction Cell Embeddings Accessor
                        Function
GetCentroids            Get cell centroids
GetClusters             Get Cluster Assignments
GetDimReduction         Dimensional Reduction Accessor Function
GetGeneLoadings         Dimensional Reduction Gene Loadings Accessor
                        Function
GetIdent                Get identity of cells
HTODemux                Demultiplex samples based on data from cell
                        'hashing'
HTOHeatmap              Hashtag oligo heatmap
HoverLocator            Hover Locator
ICAEmbed                ICA Cell Embeddings Accessor Function
ICALoad                 ICA Gene Loadings Accessor Function
ICAPlot                 Plot ICA map
ICHeatmap               Independent component heatmap
ICTopCells              Find cells with highest ICA scores
ICTopGenes              Find genes with highest ICA scores
InitialMapping          Infer spatial origins for single cells
JackStraw               Determine statistical significance of PCA
                        scores.
JackStrawPlot           JackStraw Plot
KClustDimension         Perform spectral k-means clustering on single
                        cells
KMeansHeatmap           Plot k-means clusters
LogNormalize            Normalize raw data
LogVMR                  Calculate the variance to mean ratio of logged
                        values
MASTDETest              Differential expression using MAST
MakeSparse              Make object sparse
MarkerTest              ROC-based marker discovery
MatrixRowShuffle        Independently shuffle values within each row of
                        a matrix
MergeNode               Merge childen of a node
MergeSeurat             Merge Seurat Objects
MetageneBicorPlot       Plot CC bicor saturation plot
MinMax                  Apply a ceiling and floor to all values in a
                        matrix
MultiModal_CCA          Run Canonical Correlation Analysis (CCA) on
                        multimodal data
MultiModal_CIA          Run coinertia analysis on multimodal data
NegBinomDETest          Negative binomial test for UMI-count based data
NegBinomRegDETest       Negative binomial test for UMI-count based data
                        (regularized version)
NormalizeData           Normalize Assay Data
NumberClusters          Convert the cluster labels to a numeric
                        representation
OldDoHeatmap            Gene expression heatmap
PCAEmbed                PCA Cell Embeddings Accessor Function
PCALoad                 PCA Gene Loadings Accessor Function
PCAPlot                 Plot PCA map
PCASigGenes             Significant genes from a PCA
PCElbowPlot             Quickly Pick Relevant PCs
PCHeatmap               Principal component heatmap
PCTopCells              Find cells with highest PCA scores
PCTopGenes              Find genes with highest PCA scores
PlotClusterTree         Plot phylogenetic tree
PoissonDETest           Poisson test for UMI-count based data
PrintAlignSubspaceParams
                        Print AlignSubspace Calculation Parameters
PrintCCAParams          Print CCA Calculation Parameters
PrintCalcParams         Print the calculation
PrintCalcVarExpRatioParams
                        Print Parameters Associated with
                        CalcVarExpRatio
PrintDMParams           Print Diffusion Map Calculation Parameters
PrintDim                Print the results of a dimensional reduction
                        analysis
PrintFindClustersParams
                        Print FindClusters Calculation Parameters
PrintICA                Print the results of a ICA analysis
PrintICAParams          Print ICA Calculation Parameters
PrintPCA                Print the results of a PCA analysis
PrintPCAParams          Print PCA Calculation Parameters
PrintSNNParams          Print SNN Construction Calculation Parameters
PrintTSNEParams         Print TSNE Calculation Parameters
ProjectDim              Project Dimensional reduction onto full dataset
ProjectPCA              Project Principal Components Analysis onto full
                        dataset
PurpleAndYellow         A purple and yellow color palette
Read10X                 Load in data from 10X
Read10X_h5              Read 10X hdf5 file
RefinedMapping          Quantitative refinement of spatial inferences
RemoveFromTable         Remove data from a table
RenameCells             Rename cells
RenameIdent             Rename one identity class to another
ReorderIdent            Reorder identity classes
RidgePlot               Single cell ridge plot
RunCCA                  Perform Canonical Correlation Analysis
RunDiffusion            Run diffusion map
RunICA                  Run Independent Component Analysis on gene
                        expression
RunMultiCCA             Perform Canonical Correlation Analysis with
                        more than two groups
RunPCA                  Run Principal Component Analysis on gene
                        expression using IRLBA
RunPHATE                Run PHATE
RunTSNE                 Run t-distributed Stochastic Neighbor Embedding
RunUMAP                 Run UMAP
SampleUMI               Sample UMI
SaveClusters            Save cluster assignments to a TSV file
ScaleData               Scale and center the data.
ScaleDataR              Old R based implementation of ScaleData. Scales
                        and centers the data
SetAllIdent             Switch identity class definition to another
                        variable
SetAssayData            Assay Data Mutator Function
SetClusters             Set Cluster Assignments
SetDimReduction         Dimensional Reduction Mutator Function
SetIdent                Set identity class information
Seurat-deprecated       Deprecated function(s) in the Seurat package
Shuffle                 Shuffle a vector
SplitDotPlotGG          Split Dot plot visualization
SplitObject             Splits object into a list of subsetted objects.
StashIdent              Set identity class information
SubsetByPredicate       Return a subset of the Seurat object.
SubsetColumn            Return a subset of columns for a matrix or data
                        frame
SubsetData              Return a subset of the Seurat object
SubsetRow               Return a subset of rows for a matrix or data
                        frame
TSNEPlot                Plot tSNE map
TobitTest               Differential expression testing using Tobit
                        models
TransferIdent           Transfer identity class information (or meta
                        data) from one object to another
UpdateSeuratObject      Update old Seurat object to accomodate new
                        features
ValidateClusters        Cluster Validation
ValidateSpecificClusters
                        Specific Cluster Validation
VariableGenePlot        View variable genes
VizDimReduction         Visualize Dimensional Reduction genes
VizICA                  Visualize ICA genes
VizPCA                  Visualize PCA genes
VlnPlot                 Single cell violin plot
WhichCells              Identify cells matching certain criteria
WilcoxDETest            Differential expression using Wilcoxon Rank Sum
cc.genes                Cell cycle genes
pbmc_small              A small example version of the PBMC dataset
seurat                  The Seurat Class
