The Centroids Class
Centroids Methods
Get SeuratCommands
Check layers names for the input list
Get tissue coordinates
Crop Coordinates
Get and Set the Default FOV
Create a DimReduc object
Create a Centroids Objects
Generate a Class Key
Default Layer
Dimensional Reduction Validity
Default Assay
Get image data
Cell and Feature Names
Cast Assay Layers
Create a v5 Assay object
Overlay Spatial Objects Over One Another
Get Cell Embeddings
Create Spatial Coordinates
Create an Assay object
The Field of View Object
Is an object global/persistent?
The Segmentation Class
Extract delimiter information from a string.
Check if a matrix is empty
Check the Use of Dots
Is a Matrix Sparse
Check Matrix Validity
The Graph Class
Default Layer
The JackStrawData Class
Get and set feature loadings
Get and set JackStraw information
Pull spatial image names
Get cell names grouped by identity class
Check features names format
Cell and Feature Names
Check the existence of a package
A Logical Map
Conditional Garbage Collection
Stitch Matrices Together
Save and Load Seurat Objects from Rds files
Polygon Vertices
Log a command
Empty Data Frames
Radian/Degree Conversions
Create a Molecules Object
The Dimensional Reduction Class
Rename assays in a Seurat object
Get, set, and manipulate an object's identity classes
Seurat Object Validity
FOV Validity
Assay-Level Feature and Cell Names
Get and set object keys
Create a Segmentation Objects
Register Sparse Matrix Classes
Query and Manipulate Assay Layers
FOV Methods
Create a Seurat object
Get Neighbor nearest neighbor index matrices
Query and Manipulate Assay Layers
Get and set miscellaneous data
Core Assay Infrastructure
Match Cells
Get and set miscellaneous data
A Mixin for Keyed objects
Logical Map Validity
Access cellular data
Split and Join Layers Together
Get the offset angle
Feature and Cell Numbers
Default Assay
Find the default DimReduc
Segmentation Methods
Get the Subobject Names
Query Specific Object Types
Rename cells
Neighbor Methods
Key Validity
Simplify Geometry
Find Sub-objects of a Certain Class
Get the Neighbor nearest neighbors distance matrix
Get the standard deviations for an object
.DollarNames.SeuratCommand
Dollar-sign Autocompletion
S4/List Conversion
Get and Set Additional Tool Data
The SeuratCommand Class
Dimensional Reduction Meta-Information
Generate empty dgC sparse matrix
Get Neighbor algorithm index
The Spatial Molecules Class
Generate a random name
The Neighbor class
JackStrawData Methods
Coerce Logical Maps to Matrices
Convert Segmentation Layers
Identify cells matching certain criteria
Seurat Options
Layer Data
Check List Names
SeuratObject: Data Structures for Single Cell Data
Cast to Sparse
Aggregate Molecules into an Expression Matrix
Feature-Level Meta Data
Assay-Level Feature and Cell Names
Layer Data
Update old Seurat object to accommodate new features
Coerce to a Graph Object
Find Subobjects Of A Certain Class
Assay Class Label
Layer Data
Highly Variable Features
Get Version Information
Get Parent S4 Classes
Layer Data
Drop Unused Logical Map Values
V5 Assay Summaries
Find A Subobject
Coerce to a Neighbor Object
Feature and Cell Numbers
Combine and Select Features
Feature and Cell Numbers
Disk Loading Function
Get and set project information
Molecules Methods
[[<-,Seurat,character,missing,StdAssay-method
Add Subobjects
SpatialImage methods
Update slots in an object
Layer Data
Assay-Level Feature and Cell Names
Split an Assay
Split an Assay
Feature-Level Meta Data
Calculate nCount and nFeature
[[,LogMap,integer,missing-method
LogMap Interaction Methods
Get the spot radius from an image
V5 Assay Validity
Feature-Level Meta Data
The Seurat Class
Identify Object Collections
BPCells Matrix Mode
Get a Method
Objects exported from other packages
Test Future Compatibility with Seurat
Dollar-sign Autocompletion
Rename cells
Row and Column Sums and Means
Feature and Cell Names
Check Feature Margin
Merge Sparse Matrices by Row
Generic Assay Creation
Subset an Assay
Identify Sparse Slots
The SpatialImage class
Command Log Parameter Access
Coerce to a Seurat Object
Cell-Level Meta Data
VariableFeatures-StdAssay
Highly Variable Features
Find Observations by Value
Add Subobjects
Matrix-like Subsetting for Logical Maps
Find Common Logical Map Values
Set If or If Not NA
Dollar-sign Autocompletion
Dollar-sign Autocompletion
Graph Object Overview
Get the Margin of an Object
Propagate a List
Coerce a SeuratCommand to a list
Generate a Random Key
Get the Package that Defines a Class
Feature and Cell Numbers
LogMap Object Overview
Row and Column Sums and Means
Original double-bracket assign
Merge Assays
The Seurat Class
V3 Assay Overview
A small example version of the PBMC dataset
Dollar-sign Autocompletion
Regex Pattern for Keys
Find the Default FOV
Old Seurat Object Overview
Merge Assays
Remove Subobjects and Cell-Level Meta Data
V5 Assay Overview
Set If or If Not NULL
Get Feature Loadings
Command Log Data Access
Print Top Feature Loadings
Split an Assay
Dimensional Reduction Overview
Split an Assay
Subobject Names
Merge Dimensional Reductions
Deprecate Functions and Arguments
Get Cell Embeddings
Merge Seurat Objects
Find a File Path
Move Files and Directories
show,SeuratCommand-method
Command Log Overview
Layer Data
Subobjects and Cell-Level Meta Data
Seurat Object Overview
Subset Seurat Objects
Subset an Assay
Subset a Dimensional Reduction
Subset an Assay
Merge Assays
Get and Set Assay Data
Add in metadata associated with either cells or features.
The v5 Assay Object
Attach Required Packages
Add in metadata associated with either cells or features.
The Assay Class
V5 Assay Validity
V3 Assay Validity
Get, Set, and Query Segmentation Boundaries
Get a vector of cell names associated with an image (or set of images)
Get and Set Assay Data
The Transposed v5 Assay Object
Cast Assay Layers