ALRAChooseKPlot         ALRA Approximate Rank Selection Plot
AddMetaData             Add in metadata associated with either cells or
                        features.
AddModuleScore          Calculate module scores for feature expression
                        programs in single cells
AnchorSet-class         The AnchorSet Class
Assay-class             The Assay Class
AugmentPlot             Augments ggplot2-based plot with a PNG image.
AverageExpression       Averaged feature expression by identity class
BarcodeInflectionsPlot
                        Plot the Barcode Distribution and Calculated
                        Inflection Points
BlackAndWhite           Create a custom color palette
BuildClusterTree        Phylogenetic Analysis of Identity Classes
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                   Get cells present in an object
CollapseSpeciesExpressionMatrix
                        Slim down a multi-species expression matrix,
                        when only one species is primarily of
                        interenst.
CombinePlots            Combine ggplot2-based plots into a single plot
Command                 Get SeuratCommands
CreateAssayObject       Create an Assay object
CreateDimReducObject    Create a DimReduc object
CreateGeneActivityMatrix
                        Convert a peak matrix to a gene activity matrix
CreateSeuratObject      Create a Seurat object
CustomDistance          Run a custom distance function on an input data
                        matrix
DefaultAssay            Get and set the default assay
DietSeurat              Slim down a Seurat object
DimHeatmap              Dimensional reduction heatmap
DimPlot                 Dimensional reduction plot
DimReduc-class          The Dimmensional Reduction Class
DoHeatmap               Feature expression heatmap
DotPlot                 Dot plot visualization
ElbowPlot               Quickly Pick Relevant Dimensions
Embeddings              Get cell embeddings
ExpMean                 Calculate the mean of logged values
ExpSD                   Calculate the standard deviation of logged
                        values
ExpVar                  Calculate the variance of logged values
ExportToCellbrowser     Export Seurat object for UCSC cell browser
FeaturePlot             Visualize 'features' on a dimensional reduction
                        plot
FeatureScatter          Scatter plot of single cell data
FetchData               Access cellular data
FindAllMarkers          Gene expression markers for all identity
                        classes
FindClusters            Cluster Determination
FindConservedMarkers    Finds markers that are conserved between the
                        groups
FindIntegrationAnchors
                        Find integration anchors
FindMarkers             Gene expression markers of identity classes
FindNeighbors           SNN Graph Construction
FindTransferAnchors     Find transfer anchors
FindVariableFeatures    Find variable features
GetAssay                Get an Assay object from a given Seurat object.
GetAssayData            General accessor function for the Assay class
GetIntegrationData      Get integation data
Graph-class             The Graph Class
HTODemux                Demultiplex samples based on data from cell
                        'hashing'
HTOHeatmap              Hashtag oligo heatmap
HVFInfo                 Get highly variable feature information
HoverLocator            Hover Locator
Idents                  Get, set, and manipulate an object's identity
                        classes
IntegrateData           Integrate data
IntegrationData-class   The IntegrationData Class
JS                      Get JackStraw information
JackStraw               Determine statistical significance of PCA
                        scores.
JackStrawData-class     The JackStrawData Class
JackStrawPlot           JackStraw Plot
Key                     Get a key
L2CCA                   L2-Normalize CCA
L2Dim                   L2-normalization
LabelClusters           Label clusters on a ggplot2-based scatter plot
LabelPoints             Add text labels to a ggplot2 plot
Loadings                Get feature loadings
LocalStruct             Calculate the local structure preservation
                        metric
LogNormalize            Normalize raw data
LogSeuratCommand        Log a command
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)
MetaFeature             Aggregate expression of multiple features into
                        a single feature
MinMax                  Apply a ceiling and floor to all values in a
                        matrix
Misc                    Access miscellaneous data
MixingMetric            Calculates a mixing metric
NormalizeData           Normalize Data
OldWhichCells           Identify cells matching certain criteria
PCASigGenes             Significant genes from a PCA
PercentageFeatureSet    Calculate the percentage of all counts that
                        belong to a given set of features
PlotClusterTree         Plot clusters as a tree
PolyDimPlot             Polygon DimPlot
PolyFeaturePlot         Polygon FeaturePlot
Project                 Get and set project information
ProjectDim              Project Dimensional reduction onto full dataset
Read10X                 Load in data from 10X
Read10X_h5              Read 10X hdf5 file
ReadAlevin              Load in data from Alevin pipeline
ReadAlevinCsv           Load in data from Alevin pipeline
ReadH5AD                Read from and write to h5ad files
RelativeCounts          Normalize raw data to fractions
RenameCells             Rename cells
RidgePlot               Single cell ridge plot
RunALRA                 Run Adaptively-thresholded Low Rank
                        Approximation (ALRA)
RunCCA                  Perform Canonical Correlation Analysis
RunICA                  Run Independent Component Analysis on gene
                        expression
RunLSI                  Run Latent Semantic Indexing on binary count
                        matrix
RunPCA                  Run Principal Component Analysis
RunTSNE                 Run t-distributed Stochastic Neighbor Embedding
RunUMAP                 Run UMAP
SCTransform             Use regularized negative binomial regression to
                        normalize UMI count data
SampleUMI               Sample UMI
ScaleData               Scale and center the data.
ScoreJackStraw          Compute Jackstraw scores significance.
SelectIntegrationFeatures
                        Select integration features
SetAssayData            Setter for multimodal data
SetIntegrationData      Set integation data
Seurat-class            The Seurat Class
Seurat-package          Tools for single-cell genomics
SeuratCommand-class     The SeuratCommand Class
SeuratTheme             Seurat Themes
SplitObject             Splits object into a list of subsetted objects.
Stdev                   Get the standard deviations for an object
StopCellbrowser         Stop Cellbrowser web server
SubsetByBarcodeInflections
                        Subset a Seurat Object based on the Barcode
                        Distribution Inflection Points
SubsetData              Return a subset of the Seurat object
TF.IDF                  Term frequency-inverse document frequency
Tool                    Get and set additional tool data
TopCells                Find cells with highest scores for a given
                        dimensional reduction technique
TopFeatures             Find features with highest scores for a given
                        dimensional reduction technique
TransferData            Transfer Labels
UpdateSeuratObject      Update old Seurat object to accomodate new
                        features
VariableFeaturePlot     View variable features
VariableFeatures        Get and set variable feature information
VizDimLoadings          Visualize Dimensional Reduction genes
VlnPlot                 Single cell violin plot
WhichCells              Identify cells matching certain criteria
[.Seurat                Subset a Seurat object
as.Graph                Convert a matrix (or Matrix) to the Graph
                        class.
as.Seurat               Convert objects to Seurat objects
as.SingleCellExperiment
                        Convert objects to SingleCellExperiment objects
as.loom                 Convert objects to loom objects
as.sparse               Convert between data frames and sparse matrices
cc.genes                Cell cycle genes
merge.Assay             Merge Seurat Objects
pbmc_small              A small example version of the PBMC dataset
print.DimReduc          Print the results of a dimensional reduction
                        analysis
seurat-class            The Seurat Class
