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SeuratObject (version 5.2.0)

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.

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Install

install.packages('SeuratObject')

Monthly Downloads

49,412

Version

5.2.0

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

August 27th, 2025

Functions in SeuratObject (5.2.0)

Cast Assay Layers

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

Get, Set, and Query Segmentation Boundaries

Check the Use of Dots

CellsByIdentities

Get cell names grouped by identity class

Cell and Feature Names

Centroids-class

The Centroids Class

Centroids-methods

Centroids Methods

Cell and Feature Names

CastAssay-StdAssay

Cast Assay Layers

CreateCentroids

Create a Centroids Objects

Generate a Class Key

CreateAssayObject

Create an Assay object

Conditional Garbage Collection

CheckLayersName

Check layers names for the input list

Get SeuratCommands

CreateAssay5Object

Create a v5 Assay object

CreateDimReducObject

Create a DimReduc object

CheckFeaturesNames

Check features names format

Check Matrix Validity

DefaultDimReduc

Find the default DimReduc

Get and Set the Default FOV

CreateSegmentation

Create a Segmentation Objects

Crop Coordinates

CreateMolecules

Create a Molecules Object

Create Spatial Coordinates

DefaultAssay-StdAssay

CreateSeuratObject

Create a Seurat object

DefaultLayer-StdAssay

The Field of View Object

DimReduc-validity

Dimensional Reduction Validity

The Dimensional Reduction Class

Extract delimiter information from a string.

Access cellular data

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

Pull spatial image names

Get Cell Embeddings

Get the Neighbor nearest neighbors distance matrix

Get Neighbor nearest neighbor index matrices

Is an object global/persistent?

Find Sub-objects of a Certain Class

GetTissueCoordinates

Get tissue coordinates

Check if a matrix is empty

A Mixin for Keyed objects

JackStrawData-class

The JackStrawData Class

Check List Names

Get and set object keys

Layers-StdAssay

Query and Manipulate Assay Layers

Empty Data Frames

Get and set JackStraw information

Get and set feature loadings

Molecules-class

The Spatial Molecules Class

JackStrawData-methods

JackStrawData Methods

The Graph Class

Molecules-methods

Molecules Methods

Query and Manipulate Assay Layers

Is a Matrix Sparse

Get and set miscellaneous data

Get and set miscellaneous data

The Neighbor class

Neighbor-methods

Neighbor Methods

Generate a random name

Get the spot radius from an image

Get Neighbor algorithm index

LogSeuratCommand

Overlay Spatial Objects Over One Another

LogMap-validity

Logical Map Validity

Check the existence of a package

Get and set project information

Polygon Vertices

Query Specific Object Types

RowMergeSparseMatrices

Merge Sparse Matrices by Row

Rename assays in a Seurat object

Segmentation-class

The Segmentation Class

RegisterSparseMatrix

Register Sparse Matrix Classes

RenameCells-StdAssay

Segmentation-validity

Segmentation Validity

Save and Load Seurat Objects from Rds files

Segmentation-methods

Segmentation Methods

Seurat-validity

Seurat Object Validity

SeuratCommand-class

The SeuratCommand Class

SpatialImage-methods

SpatialImage methods

SeuratObject-options

SpatialImage-class

The SpatialImage class

Split and Join Layers Together

The Seurat Class

Simplify Geometry

Core Assay Infrastructure

SparseEmptyMatrix

Generate empty dgC sparse matrix

Get the standard deviations for an object

SeuratObject-package

SeuratObject: Data Structures for Single Cell Data

Stitch Matrices Together

Get Version Information

Get the offset angle

Highly Variable Features

StdAssay-validity

V5 Assay Validity

Update slots in an object

UpdateSeuratObject

Update old Seurat object to accommodate new features

Get and Set Additional Tool Data

VariableFeatures-StdAssay

Highly Variable Features

Coerce to a Graph Object

as.list.SeuratCommand

Coerce a SeuratCommand to a list

Coerce to a Neighbor Object

Coerce to a Seurat Object

Aggregate Molecules into an Expression Matrix

Convert Segmentation Layers

Radian/Degree Conversions

Identify cells matching certain criteria

Feature and Cell Numbers

colMeans,Assay-method

Row and Column Sums and Means

colMeans,Seurat-method

Row and Column Sums and Means

as.matrix.LogMap

Coerce Logical Maps to Matrices

Cell-Level Meta Data

$.SeuratCommand

Command Log Parameter Access

Feature and Cell Numbers

dimnames.Seurat

Feature and Cell Names

Dimensional Reduction Meta-Information

BPCells Matrix Mode

dimnames.Assay5

Assay-Level Feature and Cell Names

Assay-Level Feature and Cell Names

dimnames.StdAssay

Assay-Level Feature and Cell Names

Assay Class Label

Feature and Cell Numbers

Feature and Cell Numbers

Check Feature Margin

Calculate nCount and nFeature

Disk Loading Function

Get Parent S4 Classes

Identify Object Collections

.DollarNames.Assay

Dollar-sign Autocompletion

Get the Package that Defines a Class

.CreateStdAssay

Generic Assay Creation

Find A Subobject

Find Subobjects Of A Certain Class

.DollarNames.Assay5

Dollar-sign Autocompletion

.DollarNames.Seurat

Dollar-sign Autocompletion

Find the Default FOV

Deprecate Functions and Arguments

.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.

.DollarNames.SeuratCommand

Dollar-sign Autocompletion

Generate a Random Key

.DollarNames.StdAssay

Dollar-sign Autocompletion

Propagate a List

Find Observations by Value

Regex Pattern for Keys

.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.

.IsFutureSeurat

Test Future Compatibility with Seurat

Move Files and Directories

Get the Margin of an Object

Find a File Path

intersect.LogMap

Find Common Logical Map Values

droplevels.LogMap

Drop Unused Logical Map Values

Merge Seurat Objects

Subobject Names

Print Top Feature Loadings

Original double-bracket assign

The Seurat Class

Identify Sparse Slots

Get the Subobject Names

Merge Dimensional Reductions

A small example version of the PBMC dataset

Objects exported from other packages

show,SeuratCommand-method

Command Log Overview

Set If or If Not NULL

Set If or If Not NA

show,Assay-method

V3 Assay Overview

S4/List Conversion

show,DimReduc-method

Dimensional Reduction Overview

show,StdAssay-method

V5 Assay Overview

show,Graph-method

Graph Object Overview

show,LogMap-method

LogMap Object Overview

show,Seurat-method

Seurat Object Overview

Get Feature Loadings

show,seurat-method

Old Seurat Object Overview

[.SeuratCommand

Command Log Data Access

Feature-Level Meta Data

Subobjects and Cell-Level Meta Data

Matrix-like Subsetting for Logical Maps

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

Get Cell Embeddings

Feature-Level Meta Data

subset.DimReduc

Subset a Dimensional Reduction

Feature-Level Meta Data

Subset Seurat Objects

[[,LogMap,integer,missing-method

LogMap Interaction Methods

[[<-,Seurat,NULL

Remove Subobjects and Cell-Level Meta Data

Subset an Assay

Subset an Assay

subset.StdAssay

Subset an Assay

v5-assay-summaries

V5 Assay Summaries

Add in metadata associated with either cells or features.

Assay5-validity

V5 Assay Validity

Get and Set Assay Data

The Transposed v5 Assay Object

The Assay Class

Attach Required Packages

V3 Assay Validity

The v5 Assay Object

AssayData-StdAssay

Get and Set Assay Data

AddMetaData-StdAssay

Add in metadata associated with either cells or features.