$.Assay                 Layer Data
$.Assay5                Layer Data
$.Seurat                Cell-Level Meta Data
$.SeuratCommand         Command Log Parameter Access
.DollarNames.SeuratCommand
                        Dollar-sign Autocompletion
AddMetaData             Add in metadata associated with either cells or
                        features.
Assay-class             The Assay Class
Assay-validity          V3 Assay Validity
Assay5-class            The v5 'Assay' Object
Assay5-validity         V5 Assay Validity
AssayData               Get and Set Assay Data
Assays                  Query Specific Object Types
AttachDeps              Attach Required Packages
Boundaries              Get, Set, and Query Segmentation Boundaries
CastAssay               Cast Assay Layers
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
CheckLayersName         Check layers names for the input list
Command                 Get SeuratCommands
CreateAssay5Object      Create a v5 Assay object
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<-       Set Default Dimensionality Reduction Set the
                        default dimensionality reduction for a specific
                        assay in a Seurat object.
DefaultFOV              Get and Set the Default FOV
DefaultLayer            Default Layer
DimReduc-class          The Dimensional Reduction Class
DimReduc-validity       Dimensional Reduction Validity
Distances               Get the Neighbor nearest neighbors distance
                        matrix
Embeddings              Get Cell Embeddings
EmptyMatrix             Empty Matrices
FOV-class               The Field of View Object
FOV-methods             'FOV' Methods
FOV-validity            FOV Validity
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
JoinLayers              Split and Join Layers Together
Key                     Get and set object keys
LayerData               Query and Manipulate Assay Layers
Loadings                Get and set feature loadings
LogMap                  A Logical Map
LogMap-validity         Logical Map Validity
LogSeuratCommand        Log a command
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
SaveSeuratRds           Save and Load 'Seurat' Objects from Rds files
Segmentation-class      The 'Segmentation' Class
Segmentation-methods    'Segmentation' Methods
Segmentation-validity   Segmentation Validity
Seurat-class            The Seurat Class
Seurat-validity         Seurat Object Validity
SeuratCommand-class     The 'SeuratCommand' Class
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
StitchMatrix            Stitch Matrices Together
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
[.Assay                 Layer Data
[.Assay5                Layer Data
[.DimReduc              Get Feature Loadings
[.SeuratCommand         Command Log Data Access
[[.Assay                Feature-Level Meta Data
[[.Assay5               Feature-Level Meta Data
[[.DimReduc             Get Cell Embeddings
[[.Seurat               Subobjects and Cell-Level Meta Data
[[<-,Seurat             Add Subobjects
[[<-,Seurat,NULL        Remove Subobjects and Cell-Level Meta Data
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.list.SeuratCommand   Coerce a 'SeuratCommand' to a list
as.matrix.LogMap        Coerce Logical Maps to Matrices
as.sparse               Cast to Sparse
dim.Assay               Feature and Cell Numbers
dim.Assay5              Feature and Cell Numbers
dim.DimReduc            Dimensional Reduction Meta-Information
dim.Seurat              Feature and Cell Numbers
dimnames.Assay          Assay-Level Feature and Cell Names
dimnames.Assay5         Assay-Level Feature and Cell Names
dimnames.Seurat         Feature and Cell Names
droplevels.LogMap       Drop Unused Logical Map Values
intersect.LogMap        Find Common Logical Map Values
labels.LogMap           Find Observations by Value
merge.Assay             Merge Assays
merge.Assay5            Merge Assays
merge.DimReduc          Merge Dimensional Reductions
merge.Seurat            Merge Seurat Objects
names.Seurat            Subobject Names
pbmc_small              A small example version of the PBMC dataset
print.DimReduc          Print Top Feature Loadings
set-if-null             Set If or If Not 'NULL'
show,LogMap-method      'LogMap' Object Overview
split.Assay             Split an Assay
split.Assay5            Split an Assay
subset.Assay            Subset an Assay
subset.Assay5           Subset an Assay
subset.DimReduc         Subset a Dimensional Reduction
subset.Seurat           Subset 'Seurat' Objects
