AddMetaData             Add in metadata associated with either cells or
                        features.
Assay-class             The Assay Class
Assay-methods           'Assay' Methods
AssayData               Get and Set Assay Data
Assays                  Query Specific Object Types
AttachDeps              Attach Required Packages
Boundaries              Get, Set, and Query Segmentation Boundaries
Cells                   Cell and Feature Names
CellsByIdentities       Get cell names grouped by identity class
CellsByImage            Get a vector of cell names associated with an
                        image (or set of images)
Centroids-class         The 'Centroids' Class
Centroids-methods       'Centroids' Methods
CheckGC                 Conditional Garbage Collection
Command                 Get SeuratCommands
CreateAssayObject       Create an Assay object
CreateCentroids         Create a 'Centroids' Objects
CreateDimReducObject    Create a DimReduc object
CreateFOV               Create Spatial Coordinates
CreateMolecules         Create a 'Molecules' Object
CreateSegmentation      Create a 'Segmentation' Objects
CreateSeuratObject      Create a 'Seurat' object
Crop                    Crop Coordinates
DefaultAssay            Default Assay
DefaultDimReduc         Find the default 'DimReduc'
DefaultFOV              Get and Set the Default FOV
DimReduc-class          The Dimensional Reduction Class
DimReduc-methods        'DimReduc' Methods
Distances               Get the Neighbor nearest neighbors distance
                        matrix
Embeddings              Get Cell Embeddings
FOV-class               The Field of View Object
FOV-methods             'FOV' Methods
FetchData               Access cellular data
FilterObjects           Find Sub-objects of a Certain Class
GetImage                Get image data
GetTissueCoordinates    Get tissue coordinates
Graph-class             The Graph Class
HVFInfo                 Highly Variable Features
Idents                  Get, set, and manipulate an object's identity
                        classes
Images                  Pull spatial image names
Index                   Get Neighbor algorithm index
Indices                 Get Neighbor nearest neighbor index matrices
IsGlobal                Is an object global/persistent?
IsMatrixEmpty           Check if a matrix is empty
IsNamedList             Check List Names
JS                      Get and set JackStraw information
JackStrawData-class     The JackStrawData Class
JackStrawData-methods   'JackStrawData' Methods
Key                     Get and set object keys
Loadings                Get and set feature loadings
LogMap-class            A Logical Map
LogSeuratCommand        Log a command
MatchCells              Match Cells
Misc                    Get and set miscellaneous data
Molecules-class         The Spatial Molecules Class
Molecules-methods       'Molecules' Methods
Neighbor-class          The Neighbor class
Neighbor-methods        'Neighbor' Methods
Overlay                 Overlay 'Spatial' Objects Over One Another
PackageCheck            Check the existence of a package
Project                 Get and set project information
Radius                  Get the spot radius from an image
RandomName              Generate a random name
RenameAssays            Rename assays in a 'Seurat' object
RenameCells             Rename cells
RowMergeSparseMatrices
                        Merge Sparse Matrices by Row
Segmentation-class      The 'Segmentation' Class
Segmentation-methods    'Segmentation' Methods
Seurat-class            The Seurat Class
Seurat-methods          Seurat Methods
SeuratCommand-class     The SeuratCommand Class
SeuratCommand-methods   'SeuratCommand' Methods
SeuratObject-package    SeuratObject: Data Structures for Single Cell
                        Data
Simplify                Simplify Geometry
SpatialImage-class      The SpatialImage class
SpatialImage-methods    'SpatialImage' methods
Stdev                   Get the standard deviations for an object
Theta                   Get the offset angle
Tool                    Get and set additional tool data
UpdateSeuratObject      Update old Seurat object to accommodate new
                        features
UpdateSlots             Update slots in an object
Version                 Get Version Information
WhichCells              Identify cells matching certain criteria
aggregate               Aggregate Molecules into an Expression Matrix
as.Centroids            Convert Segmentation Layers
as.Graph                Coerce to a 'Graph' Object
as.Neighbor             Coerce to a 'Neighbor' Object
as.Seurat               Coerce to a 'Seurat' Object
as.sparse               Cast to Sparse
pbmc_small              A small example version of the PBMC dataset
s4list                  S4/List Conversion
set-if-na               Set if 'NA'
