Learn R Programming

SeuratObject (version 5.3.0)

Data Structures for Single Cell Data

Description

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) , Macosko E, Basu A, Satija R, et al (2015) , and Stuart T, Butler A, et al (2019) , Hao Y, Hao S, et al (2021) and Hao Y, et al (2023) for more details.

Copy Link

Version

Install

install.packages('SeuratObject')

Monthly Downloads

59,765

Version

5.3.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/satijalab/seurat-object

Homepage

https://satijalab.github.io/seurat-object/

Maintainer

Paul Hoffman

Last Published

December 12th, 2025

Functions in SeuratObject (5.3.0)

Get, Set, and Query Segmentation Boundaries

CreateAssay5Object

Create a v5 Assay object

CastAssay-StdAssay

Cast Assay Layers

CellsByIdentities

Get cell names grouped by identity class

Cell and Feature Names

CreateCentroids

Create a Centroids Objects

Get SeuratCommands

DefaultAssay-StdAssay

Crop Coordinates

Generate a Class Key

CheckLayersName

Check layers names for the input list

Create Spatial Coordinates

CreateMolecules

Create a Molecules Object

CreateDimReducObject

Create a DimReduc object

Get Cell Embeddings

Check Matrix Validity

DefaultDimReduc

Find the default DimReduc

CreateSegmentation

Create a Segmentation Objects

Conditional Garbage Collection

Cast Assay Layers

CheckFeaturesNames

Check features names format

Cell and Feature Names

Get Neighbor nearest neighbor index matrices

The Dimensional Reduction Class

Get and Set the Default FOV

Get the Neighbor nearest neighbors distance matrix

DimReduc-validity

Dimensional Reduction Validity

DefaultLayer-StdAssay

Find Sub-objects of a Certain Class

CreateAssayObject

Create an Assay object

Empty Data Frames

The Field of View Object

Is a Matrix Sparse

Get and set JackStraw information

Get and set miscellaneous data

Is an object global/persistent?

JackStrawData-methods

JackStrawData Methods

Neighbor-methods

Neighbor Methods

Get and set miscellaneous data

The Graph Class

GetTissueCoordinates

Get tissue coordinates

CreateSeuratObject

Create a Seurat object

Extract delimiter information from a string.

Get and set object keys

Access cellular data

Get the spot radius from an image

Segmentation-methods

Segmentation Methods

LogMap-validity

Logical Map Validity

Generate a random name

Check if a matrix is empty

JackStrawData-class

The JackStrawData Class

Molecules-class

The Spatial Molecules Class

RowMergeSparseMatrices

Merge Sparse Matrices by Row

Save and Load Seurat Objects from Rds files

Simplify Geometry

Segmentation-class

The Segmentation Class

Seurat-validity

Seurat Object Validity

SparseEmptyMatrix

Generate empty dgC sparse matrix

Get, set, and manipulate an object's identity classes

Overlay Spatial Objects Over One Another

Pull spatial image names

A Mixin for Keyed objects

Get Neighbor algorithm index

Check List Names

LogSeuratCommand

The Neighbor class

Query Specific Object Types

Molecules-methods

Molecules Methods

Get and set project information

Get and Set Additional Tool Data

Convert Segmentation Layers

Segmentation-validity

Segmentation Validity

SpatialImage-class

The SpatialImage class

The Seurat Class

SeuratObject-options

Polygon Vertices

Highly Variable Features

Layers-StdAssay

Query and Manipulate Assay Layers

SeuratObject-package

SeuratObject: Data Structures for Single Cell Data

Get the standard deviations for an object

$.SeuratCommand

Command Log Parameter Access

Cell-Level Meta Data

Radian/Degree Conversions

Identify cells matching certain criteria

UpdateSeuratObject

Update old Seurat object to accommodate new features

SpatialImage-methods

SpatialImage methods

Check Feature Margin

StdAssay-validity

V5 Assay Validity

Aggregate Molecules into an Expression Matrix

Get and set feature loadings

Check the existence of a package

Query and Manipulate Assay Layers

.DollarNames.Seurat

Dollar-sign Autocompletion

RegisterSparseMatrix

Register Sparse Matrix Classes

Rename assays in a Seurat object

Split and Join Layers Together

Update slots in an object

VariableFeatures-StdAssay

Highly Variable Features

Coerce to a Seurat Object

Dimensional Reduction Meta-Information

dimnames.Seurat

Feature and Cell Names

SeuratCommand-class

The SeuratCommand Class

Feature and Cell Numbers

.DollarNames.Assay5

Dollar-sign Autocompletion

Generate a Random Key

Identify Sparse Slots

Get the Package that Defines a Class

.DollarNames.SeuratCommand

Dollar-sign Autocompletion

dimnames.StdAssay

Assay-Level Feature and Cell Names

.DollarNames.StdAssay

Dollar-sign Autocompletion

Stitch Matrices Together

RenameCells-StdAssay

Calculate nCount and nFeature

Core Assay Infrastructure

Propagate a List

Assay-Level Feature and Cell Names

dimnames.Assay5

Assay-Level Feature and Cell Names

Get Parent S4 Classes

Identify Object Collections

Get the offset angle

show,LogMap-method

LogMap Object Overview

show,SeuratCommand-method

Command Log Overview

Merge Dimensional Reductions

show,StdAssay-method

V5 Assay Overview

droplevels.LogMap

Drop Unused Logical Map Values

.CreateStdAssay

Generic Assay Creation

Move Files and Directories

Find a File Path

as.list.SeuratCommand

Coerce a SeuratCommand to a list

Set If or If Not NULL

Coerce to a Graph Object

Disk Loading Function

Print Top Feature Loadings

intersect.LogMap

Find Common Logical Map Values

Objects exported from other packages

Get Version Information

.DollarNames.Assay

Dollar-sign Autocompletion

[[<-,Seurat,character,missing,StdAssay-method

Find Observations by Value

show,DimReduc-method

Dimensional Reduction Overview

The Seurat Class

.GetConsensusFeatures

Returns the most frequently observed features in `features_by_layer`. If two features are observed at the same frequency their median index will be used to break the tie. If `nfeatures` is not specified, all features in `common_features` are returned.

Get Cell Embeddings

.IsFutureSeurat

Test Future Compatibility with Seurat

.GetVariableFeatures

Returns the top variable features from a data frame of highly variable feature annotations. Features are marked as variable if their value in `label_column` is neither `NA` nor `FALSE`. When a ranking is provided via `rank_column`, features are ordered accordingly.

A small example version of the PBMC dataset

Set If or If Not NA

S4/List Conversion

Coerce to a Neighbor Object

as.matrix.LogMap

Coerce Logical Maps to Matrices

[.SeuratCommand

Command Log Data Access

Get the Subobject Names

Merge Seurat Objects

Subset an Assay

Feature-Level Meta Data

Subset an Assay

show,Seurat-method

Seurat Object Overview

colMeans,Assay-method

Row and Column Sums and Means

Assay Class Label

Find Subobjects Of A Certain Class

show,Graph-method

Graph Object Overview

[[<-,Seurat,NULL

Remove Subobjects and Cell-Level Meta Data

[[,LogMap,integer,missing-method

LogMap Interaction Methods

colMeans,Seurat-method

Row and Column Sums and Means

Feature and Cell Numbers

Subobject Names

Feature and Cell Numbers

Feature-Level Meta Data

subset.DimReduc

Subset a Dimensional Reduction

Find the Default FOV

Feature and Cell Numbers

Original double-bracket assign

Deprecate Functions and Arguments

Matrix-like Subsetting for Logical Maps

Subset Seurat Objects

show,seurat-method

Old Seurat Object Overview

BPCells Matrix Mode

Find A Subobject

Subobjects and Cell-Level Meta Data

show,Assay-method

V3 Assay Overview

Get the Margin of an Object

Get Feature Loadings

v5-assay-summaries

V5 Assay Summaries

Feature-Level Meta Data

subset.StdAssay

Subset an Assay

Regex Pattern for Keys

The Assay Class

AddMetaData-StdAssay

Add in metadata associated with either cells or features.

Add in metadata associated with either cells or features.

V3 Assay Validity

Attach Required Packages

Get and Set Assay Data

Assay5-validity

V5 Assay Validity

The v5 Assay Object

The Transposed v5 Assay Object

AssayData-StdAssay

Get and Set Assay Data

Centroids-class

The Centroids Class

Get a vector of cell names associated with an image (or set of images)

Centroids-methods

Centroids Methods

Check the Use of Dots