Data Structures for Single Cell Data
Attach Required Packages
Get, Set, and Query Segmentation Boundaries
Layer Data
Layer Data
Simplify Geometry
Generate empty dgC sparse matrix
The SpatialImage class
SpatialImage methods
Command Log Overview
Find Subobjects Of A Certain Class
Find A Subobject
Get a Method
V5 Assay Overview
Default Layer
Feature and Cell Numbers
Feature and Cell Numbers
The Centroids Class
Extract delimiter information from a string.
Get and Set Assay Data
Rename cells
Add in metadata associated with either cells or features.
Add in metadata associated with either cells or features.
Get and Set Assay Data
Aggregate Molecules into an Expression Matrix
Radian/Degree Conversions
Convert Segmentation Layers
Coerce to a Graph Object
Coerce a SeuratCommand to a list
Coerce Logical Maps to Matrices
Coerce to a Neighbor Object
Coerce to a Seurat Object
Cast to Sparse
The Assay Class
V3 Assay Validity
The v5 Assay Object
V5 Assay Validity
The Transposed v5 Assay Object
Cell-Level Meta Data
Command Log Parameter Access
Layer Data
Cast Assay Layers
Cast Assay Layers
Cell and Feature Names
Cell and Feature Names
Get cell names grouped by identity class
Get a vector of cell names associated with an image (or set of images)
Centroids Methods
Check the Use of Dots
Check features names format
Conditional Garbage Collection
Check layers names for the input list
Check Matrix Validity
Generate a Class Key
Row and Column Sums and Means
Find the default DimReduc
Row and Column Sums and Means
Get SeuratCommands
Create a v5 Assay object
Create an Assay object
Create a Centroids Objects
Create a DimReduc object
Get and Set the Default FOV
Create Spatial Coordinates
Create a Molecules Object
Create a Segmentation Objects
Create a Seurat object
Crop Coordinates
Default Assay
Default Assay
Default Layer
Dimensional Reduction Meta-Information
Feature and Cell Numbers
Feature and Cell Numbers
Assay-Level Feature and Cell Names
Assay-Level Feature and Cell Names
Feature and Cell Names
Assay-Level Feature and Cell Names
The Dimensional Reduction Class
Dimensional Reduction Validity
Get the Neighbor nearest neighbors distance matrix
Assay Class Label
BPCells Matrix Mode
Calculate nCount and nFeature
Check Feature Margin
Get the Package that Defines a Class
Identify Object Collections
Get Parent S4 Classes
Move Files and Directories
Generic Assay Creation
Find the Default FOV
Deprecate Functions and Arguments
Disk Loading Function
Dollar-sign Autocompletion
Dollar-sign Autocompletion
Dollar-sign Autocompletion
Dollar-sign Autocompletion
Dollar-sign Autocompletion
Find a File Path
Test Future Compatibility with Seurat
Regex Pattern for Keys
Get the Margin of an Object
Propagate a List
Generate a Random Key
Combine and Select Features
Identify Sparse Slots
Get the Subobject Names
Drop Unused Logical Map Values
Get Cell Embeddings
Empty Data Frames
Empty Matrices
Access cellular data
Find Sub-objects of a Certain Class
The Field of View Object
FOV Methods
FOV Validity
Get image data
Get tissue coordinates
The Graph Class
Get, set, and manipulate an object's identity classes
Pull spatial image names
Get Neighbor nearest neighbor index matrices
Find Common Logical Map Values
Is an object global/persistent?
Check if a matrix is empty
Check List Names
Is a Matrix Sparse
The JackStrawData Class
SeuratObject: Data Structures for Single Cell Data
JackStrawData Methods
Get and set JackStraw information
Key Validity
Get and set object keys
A Mixin for Keyed objects
Find Observations by Value
V3 Assay Overview
Dimensional Reduction Overview
Query and Manipulate Assay Layers
Query and Manipulate Assay Layers
Get and set feature loadings
A Logical Map
Logical Map Validity
Log a command
Match Cells
Merge Assays
Merge Assays
Merge Dimensional Reductions
Merge Seurat Objects
Merge Assays
Get and set miscellaneous data
Get and set miscellaneous data
The Spatial Molecules Class
Molecules Methods
Subobject Names
The Neighbor class
Neighbor Methods
Get Neighbor algorithm index
Query Specific Object Types
Original double-bracket assign
The Seurat Class
Graph Object Overview
Overlay Spatial Objects Over One Another
Check the existence of a package
Polygon Vertices
Print Top Feature Loadings
Get and set project information
Get the spot radius from an image
Generate a random name
Objects exported from other packages
Register Sparse Matrix Classes
Rename assays in a Seurat object
Rename cells
Merge Sparse Matrices by Row
S4/List Conversion
Save and Load Seurat Objects from Rds files
The Segmentation Class
LogMap Object Overview
Old Seurat Object Overview
Seurat Object Overview
Segmentation Methods
Set If or If Not NA
Set If or If Not NULL
The Seurat Class
Seurat Object Validity
The SeuratCommand Class
Seurat Options
Split an Assay
Split an Assay
Split an Assay
Split an Assay
Split and Join Layers Together
Layer Data
Core Assay Infrastructure
V5 Assay Validity
Get the standard deviations for an object
Stitch Matrices Together
Layer Data
Layer Data
Get Feature Loadings
Command Log Data Access
Matrix-like Subsetting for Logical Maps
Feature-Level Meta Data
Feature-Level Meta Data
Get Cell Embeddings
Subobjects and Cell-Level Meta Data
Subset a Dimensional Reduction
Feature-Level Meta Data
LogMap Interaction Methods
Add Subobjects
Remove Subobjects and Cell-Level Meta Data
Add Subobjects
Subset an Assay
Subset an Assay
Subset Seurat Objects
Subset an Assay
Get the offset angle
Get and Set Additional Tool Data
Update old Seurat object to accommodate new features
Update slots in an object
V5 Assay Summaries
Highly Variable Features
Highly Variable Features
Get Version Information
Identify cells matching certain criteria
Defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. Provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for more details.
Useful links