Reference

The Seurat Class and Interaction Methods
Seurat-class Seurat	The Seurat Class
Seurat-validity	Seurat Object Validity
AddMetaData()	Add in metadata associated with either cells or features.
CreateSeuratObject()	Create a Seurat object
Idents() `Idents<-`() RenameIdents() ReorderIdent() SetIdent() StashIdent() droplevels(<Seurat>) levels(<Seurat>) `levels<-`(<Seurat>)	Get, set, and manipulate an object's identity classes
Project() `Project<-`()	Get and set project information
RenameAssays()	Rename assays in a Seurat object
RenameCells()	Rename cells
UpdateSeuratObject()	Update old Seurat object to accommodate new features
as.Seurat()	Coerce to a Seurat Object
`$`(<Seurat>) `$<-`(<Seurat>) `[[<-`(<Seurat>,<character>,<missing>,<data.frame>) `[[<-`(<Seurat>,<missing>,<missing>,<data.frame>) `[[<-`(<Seurat>,<character>,<missing>,<factor>) `[[<-`(<Seurat>,<character>,<missing>,<list>) `[[<-`(<Seurat>,<missing>,<missing>,<list>) `[[<-`(<Seurat>,<character>,<missing>,<vector>)	Cell-Level Meta Data
dim(<Seurat>)	Feature and Cell Numbers
dimnames(<Seurat>) `dimnames<-`(<Seurat>)	Feature and Cell Names
merge(<Seurat>)	Merge Seurat Objects
names(<Seurat>)	Subobject Names
`[[`(<Seurat>) head(<Seurat>) tail(<Seurat>)	Subobjects and Cell-Level Meta Data
`[[<-`(<Seurat>,<character>,<missing>,<NULL>)	Remove Subobjects and Cell-Level Meta Data
`[[<-`(<Seurat>,<character>,<missing>,<Assay>) `[[<-`(<Seurat>,<character>,<missing>,<Assay5>) `[[<-`(<Seurat>,<character>,<missing>,<DimReduc>) `[[<-`(<Seurat>,<character>,<missing>,<Graph>) `[[<-`(<Seurat>,<character>,<missing>,<Neighbor>) `[[<-`(<Seurat>,<character>,<missing>,<SeuratCommand>) `[[<-`(<Seurat>,<character>,<missing>,<SpatialImage>)	Add Subobjects
subset(<Seurat>) `[`(<Seurat>)	Subset Seurat Objects
The v5 Assay Class and Interaction Methods
Assay5-class Assay5	The v5 Assay Object
Assay5-validity	V5 Assay Validity
CastAssay()	Cast Assay Layers
DefaultLayer() `DefaultLayer<-`()	Default Layer
JoinLayers()	Split and Join Layers Together
`$`(<Assay5>) `$<-`(<Assay5>)	Layer Data
dim(<Assay5>)	Feature and Cell Numbers
dimnames(<Assay5>) `dimnames<-`(<Assay5>)	Assay-Level Feature and Cell Names
merge(<Assay5>)	Merge Assays
split(<Assay5>)	Split an Assay
`[`(<Assay5>) `[<-`(<Assay5>,<character>,<ANY>,<ANY>)	Layer Data
`[[`(<Assay5>) `[[<-`(<Assay5>,<ANY>,<ANY>,<ANY>) head(<Assay5>) tail(<Assay5>)	Feature-Level Meta Data
subset(<Assay5>)	Subset an Assay
The v3 Assay Class and Interaction Methods
Assay-class Assay	The Assay Class
Assay-validity	V3 Assay Validity
CreateAssay5Object()	Create a v5 Assay object
CreateAssayObject()	Create an Assay object
`$`(<Assay>) `$<-`(<Assay>)	Layer Data
dim(<Assay>)	Feature and Cell Numbers
dimnames(<Assay>) `dimnames<-`(<Assay>)	Assay-Level Feature and Cell Names
merge(<Assay>)	Merge Assays
split(<Assay>)	Split an Assay
`[`(<Assay>) `[<-`(<Assay>,<character>,<ANY>,<ANY>)	Layer Data
`[[`(<Assay>) `[[<-`(<Assay>,<ANY>,<ANY>,<ANY>) head(<Assay>) tail(<Assay>) `[[<-`(<Assay>,<missing>,<missing>,<data.frame>)	Feature-Level Meta Data
subset(<Assay>)	Subset an Assay
The DimReduc and JackStrawData Classes and Interaction Methods
DimReduc-class DimReduc	The Dimensional Reduction Class
DimReduc-validity	Dimensional Reduction Validity
CreateDimReducObject()	Create a DimReduc object
dim(<DimReduc>) dimnames(<DimReduc>) length(<DimReduc>) names(<DimReduc>)	Dimensional Reduction Meta-Information
merge(<DimReduc>)	Merge Dimensional Reductions
print(<DimReduc>)	Print Top Feature Loadings
`[`(<DimReduc>)	Get Feature Loadings
`[[`(<DimReduc>)	Get Cell Embeddings
subset(<DimReduc>)	Subset a Dimensional Reduction
JackStrawData-class JackStrawData	The JackStrawData Class
.DollarNames(<JackStrawData>) `$`(<JackStrawData>) as.logical(<JackStrawData>) show(<JackStrawData>)	JackStrawData Methods
JS() `JS<-`()	Get and set JackStraw information
Imaging-Based Spatial Classes and Methods
FOV-class FOV	The Field of View Object
Cells(<FOV>) Features(<FOV>) FetchData(<FOV>) GetTissueCoordinates(<FOV>) Keys(<FOV>) RenameCells(<FOV>) `$`(<FOV>) `[`(<FOV>) `[[`(<FOV>) length(<FOV>) names(<FOV>) subset(<FOV>) `[[<-`(<FOV>,<character>,<missing>,<Centroids>) `[[<-`(<FOV>,<character>,<missing>,<Molecules>) `[[<-`(<FOV>,<character>,<missing>,<NULL>) `[[<-`(<FOV>,<character>,<missing>,<Segmentation>) show(<FOV>)	FOV Methods
FOV-validity	FOV Validity
Centroids-class	The Centroids Class
Cells(<Centroids>) GetTissueCoordinates(<Centroids>) Radius(<Centroids>) RenameCells(<Centroids>) Theta(<Centroids>) is.finite(<Centroids>) is.infinite(<Centroids>) length(<Centroids>) lengths(<Centroids>) subset(<Centroids>) `[`(<Centroids>,<character>,<ANY>,<ANY>) `[`(<Centroids>,<numeric>,<ANY>,<ANY>) show(<Centroids>)	Centroids Methods
Molecules-class	The Spatial Molecules Class
Features(<Molecules>) GetTissueCoordinates(<Molecules>) subset(<Molecules>) show(<Molecules>)	Molecules Methods
Segmentation-class	The Segmentation Class
Cells(<Segmentation>) GetTissueCoordinates(<Segmentation>) RenameCells(<Segmentation>) lengths(<Segmentation>) subset(<Segmentation>) `[`(<Segmentation>,<ANY>,<ANY>,<ANY>) coordinates(<Segmentation>) show(<Segmentation>)	Segmentation Methods
Boundaries() DefaultBoundary() `DefaultBoundary<-`() Molecules()	Get, Set, and Query Segmentation Boundaries
CreateCentroids()	Create a Centroids Objects
CreateFOV()	Create Spatial Coordinates
CreateMolecules()	Create a Molecules Object
CreateSegmentation()	Create a Segmentation Objects
Crop()	Crop Coordinates
DefaultFOV() `DefaultFOV<-`()	Get and Set the Default FOV
Overlay()	Overlay Spatial Objects Over One Another
Simplify()	Simplify Geometry
Theta()	Get the offset angle
as.Centroids() as.Segmentation()	Convert Segmentation Layers
The SeuratCommand Class and Interaction Methods
SeuratCommand-class SeuratCommand	The SeuratCommand Class
LogSeuratCommand()	Log a command
as.list(<SeuratCommand>)	Coerce a SeuratCommand to a list
`$`(<SeuratCommand>)	Command Log Parameter Access
.DollarNames(<SeuratCommand>)	Dollar-sign Autocompletion
`[`(<SeuratCommand>)	Command Log Data Access
The SpatialImage Class and Interaction Methods
SpatialImage-class SpatialImage	The SpatialImage class
Cells(<SpatialImage>) DefaultAssay(<SpatialImage>) `DefaultAssay<-`(<SpatialImage>) GetImage(<SpatialImage>) GetTissueCoordinates(<SpatialImage>) IsGlobal(<SpatialImage>) Key(<SpatialImage>) `Key<-`(<SpatialImage>) Radius(<SpatialImage>) RenameCells(<SpatialImage>) `[`(<SpatialImage>) dim(<SpatialImage>) subset(<SpatialImage>) show(<SpatialImage>)	SpatialImage methods
Radius()	Get the spot radius from an image
The Graph and Neighbor Classes and Interaction Methods
Graph-class Graph	The Graph Class
as.Graph()	Coerce to a Graph Object
Neighbor-class Neighbor	The Neighbor class
dim(<Neighbor>) show(<Neighbor>)	Neighbor Methods
as.Neighbor()	Coerce to a Neighbor Object
Accessing and Setting Object Data
GetAssayData() SetAssayData()	Get and Set Assay Data
Cells() Features()	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)
Command()	Get SeuratCommands
DefaultAssay() `DefaultAssay<-`()	Default Assay
Distances()	Get the Neighbor nearest neighbors distance matrix
Embeddings()	Get Cell Embeddings
FetchData()	Access cellular data
GetImage()	Get image data
GetTissueCoordinates()	Get tissue coordinates
Images()	Pull spatial image names
Indices()	Get Neighbor nearest neighbor index matrices
IsGlobal()	Is an object global/persistent?
Key() Keys() `Key<-`()	Get and set object keys
LayerData() `LayerData<-`() Layers()	Query and Manipulate Assay Layers
Loadings() `Loadings<-`()	Get and set feature loadings
Misc() `Misc<-`()	Get and set miscellaneous data
Index() `Index<-`()	Get Neighbor algorithm index
Assays() Graphs() Neighbors() Reductions()	Query Specific Object Types
Stdev()	Get the standard deviations for an object
Tool() `Tool<-`()	Get and Set Additional Tool Data
HVFInfo() VariableFeatures() `VariableFeatures<-`() SVFInfo() SpatiallyVariableFeatures()	Highly Variable Features
Version()	Get Version Information
WhichCells()	Identify cells matching certain criteria
Utility Functions
`%||%` `%iff%`	Set If or If Not NULL
AttachDeps()	Attach Required Packages
CheckGC()	Conditional Garbage Collection
CheckLayersName()	Check layers names for the input list
DefaultDimReduc()	Find the default DimReduc
EmptyMatrix()	Empty Matrices
FilterObjects()	Find Sub-objects of a Certain Class
IsMatrixEmpty()	Check if a matrix is empty
IsNamedList()	Check List Names
PackageCheck()	Check the existence of a package
RandomName()	Generate a random name
RowMergeSparseMatrices()	Merge Sparse Matrices by Row
SaveSeuratRds() LoadSeuratRds()	Save and Load Seurat Objects from Rds files
StitchMatrix()	Stitch Matrices Together
UpdateSlots()	Update slots in an object
as.sparse()	Cast to Sparse
Package Information
SeuratObject SeuratObject-package	SeuratObject: Data Structures for Single Cell Data
pbmc_small	A small example version of the PBMC dataset
Logical Maps
LogMap() `[[`(<LogMap>,<character>,<missing>) `[[`(<LogMap>,<missing>,<missing>) `[[`(<LogMap>,<NULL>,<missing>) `[[<-`(<LogMap>,<character>,<missing>,<character>) `[[<-`(<LogMap>,<character>,<missing>,<integer>) `[[<-`(<LogMap>,<character>,<missing>,<NULL>) `[[<-`(<LogMap>,<character>,<missing>,<numeric>)	A Logical Map
LogMap-validity	Logical Map Validity
as.matrix(<LogMap>)	Coerce Logical Maps to Matrices
droplevels(<LogMap>)	Drop Unused Logical Map Values
intersect(<LogMap>)	Find Common Logical Map Values
labels(<LogMap>)	Find Observations by Value
show(<LogMap>)	LogMap Object Overview