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SeuratObject (version 5.0.2)

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

42,702

Version

5.0.2

License

MIT + file LICENSE

Issues

Pull Requests

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Repository

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

Homepage

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

Maintainer

Last Published

May 8th, 2024

Functions in SeuratObject (5.0.2)

Cell and Feature Names

Centroids-methods

Centroids Methods

Check the Use of Dots

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

Get, Set, and Query Segmentation Boundaries

CellsByIdentities

Get cell names grouped by identity class

Cast Assay Layers

Centroids-class

The Centroids Class

CheckLayersName

Check layers names for the input list

Cell and Feature Names

CastAssay-StdAssay

Cast Assay Layers

CreateAssayObject

Create an Assay object

CreateAssay5Object

Create a v5 Assay object

CheckFeaturesNames

Check features names format

Get SeuratCommands

Crop Coordinates

DefaultAssay-StdAssay

Generate a Class Key

CreateSeuratObject

Create a Seurat object

CreateSegmentation

Create a Segmentation Objects

Conditional Garbage Collection

Get the Neighbor nearest neighbors distance matrix

Check Matrix Validity

DimReduc-validity

Dimensional Reduction Validity

DefaultDimReduc

Find the default DimReduc

CreateMolecules

Create a Molecules Object

Create Spatial Coordinates

Get Cell Embeddings

The Dimensional Reduction Class

Extract delimiter information from a string.

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

Pull spatial image names

GetTissueCoordinates

Get tissue coordinates

The Graph Class

The Field of View Object

JackStrawData-class

The JackStrawData Class

JackStrawData-methods

JackStrawData Methods

A Mixin for Keyed objects

CreateCentroids

Create a Centroids Objects

Get and Set the Default FOV

CreateDimReducObject

Create a DimReduc object

DefaultLayer-StdAssay

Is an object global/persistent?

Get Neighbor nearest neighbor index matrices

Is a Matrix Sparse

Get and set JackStraw information

Find Sub-objects of a Certain Class

Empty Data Frames

LogSeuratCommand

Overlay Spatial Objects Over One Another

Check the existence of a package

Neighbor-methods

Neighbor Methods

Query and Manipulate Assay Layers

Get and set miscellaneous data

Check List Names

Molecules-methods

Molecules Methods

Layers-StdAssay

Query and Manipulate Assay Layers

Check if a matrix is empty

Molecules-class

The Spatial Molecules Class

Query Specific Object Types

Segmentation-class

The Segmentation Class

Get and set object keys

Get and set miscellaneous data

RenameCells-StdAssay

LogMap-validity

Logical Map Validity

Get Neighbor algorithm index

Access cellular data

Save and Load Seurat Objects from Rds files

Get and set feature loadings

RowMergeSparseMatrices

Merge Sparse Matrices by Row

Simplify Geometry

Segmentation-methods

Segmentation Methods

The Neighbor class

SeuratObject-package

SeuratObject: Data Structures for Single Cell Data

The Seurat Class

SeuratCommand-class

The SeuratCommand Class

SeuratObject-options

UpdateSeuratObject

Update old Seurat object to accommodate new features

Update slots in an object

VariableFeatures-StdAssay

Highly Variable Features

Highly Variable Features

SpatialImage-class

The SpatialImage class

Convert Segmentation Layers

SparseEmptyMatrix

Generate empty dgC sparse matrix

Radian/Degree Conversions

Aggregate Molecules into an Expression Matrix

Split and Join Layers Together

Get and set project information

SpatialImage-methods

SpatialImage methods

Rename assays in a Seurat object

Get and Set Additional Tool Data

Polygon Vertices

Get the offset angle

RegisterSparseMatrix

Register Sparse Matrix Classes

Get the spot radius from an image

Coerce to a Seurat Object

Coerce to a Neighbor Object

$.SeuratCommand

Command Log Parameter Access

Seurat-validity

Seurat Object Validity

Generate a random name

dimnames.StdAssay

Assay-Level Feature and Cell Names

StdAssay-validity

V5 Assay Validity

Core Assay Infrastructure

Get the standard deviations for an object

Cell-Level Meta Data

Identify cells matching certain criteria

Get Version Information

colMeans,Assay-method

Row and Column Sums and Means

dimnames.Seurat

Feature and Cell Names

dimnames.Assay5

Assay-Level Feature and Cell Names

Assay-Level Feature and Cell Names

Stitch Matrices Together

.DollarNames.SeuratCommand

Dollar-sign Autocompletion

as.matrix.LogMap

Coerce Logical Maps to Matrices

Identify Object Collections

Find a File Path

colMeans,Seurat-method

Row and Column Sums and Means

Find Subobjects Of A Certain Class

Feature and Cell Numbers

.DollarNames.Seurat

Dollar-sign Autocompletion

Get Parent S4 Classes

as.list.SeuratCommand

Coerce a SeuratCommand to a list

Coerce to a Graph Object

Feature and Cell Numbers

Deprecate Functions and Arguments

Assay Class Label

Feature and Cell Numbers

Dimensional Reduction Meta-Information

Feature and Cell Numbers

.IsFutureSeurat

Test Future Compatibility with Seurat

Disk Loading Function

Get the Package that Defines a Class

Find the Default FOV

Check Feature Margin

.CreateStdAssay

Generic Assay Creation

Regex Pattern for Keys

Generate a Random Key

The Seurat Class

.DollarNames.StdAssay

Dollar-sign Autocompletion

Find Observations by Value

Merge Dimensional Reductions

Subobject Names

Merge Seurat Objects

.DollarNames.Assay

Dollar-sign Autocompletion

BPCells Matrix Mode

Calculate nCount and nFeature

Find A Subobject

.SelectFeatures

Combine and Select Features

[.SeuratCommand

Command Log Data Access

.DollarNames.Assay5

Dollar-sign Autocompletion

show,seurat-method

Old Seurat Object Overview

Get the Margin of an Object

Propagate a List

Identify Sparse Slots

S4/List Conversion

Get Cell Embeddings

Feature-Level Meta Data

Get the Subobject Names

Print Top Feature Loadings

Move Files and Directories

intersect.LogMap

Find Common Logical Map Values

droplevels.LogMap

Drop Unused Logical Map Values

show,LogMap-method

LogMap Object Overview

Subobjects and Cell-Level Meta Data

show,Seurat-method

Seurat Object Overview

Set If or If Not NULL

Original double-bracket assign

A small example version of the PBMC dataset

[[,LogMap,integer,missing-method

LogMap Interaction Methods

v5-assay-summaries

V5 Assay Summaries

[[<-,Seurat,NULL

Remove Subobjects and Cell-Level Meta Data

subset.StdAssay

Subset an Assay

show,SeuratCommand-method

Command Log Overview

Objects exported from other packages

show,Assay-method

V3 Assay Overview

Get Feature Loadings

subset.DimReduc

Subset a Dimensional Reduction

Feature-Level Meta Data

Matrix-like Subsetting for Logical Maps

show,DimReduc-method

Dimensional Reduction Overview

Feature-Level Meta Data

show,StdAssay-method

V5 Assay Overview

Subset Seurat Objects

Subset an Assay

Subset an Assay

Set If or If Not NA

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

show,Graph-method

Graph Object Overview

Add in metadata associated with either cells or features.

V3 Assay Validity

The Assay Class

AddMetaData-StdAssay

Add in metadata associated with either cells or features.

The v5 Assay Object

The Transposed v5 Assay Object

Get and Set Assay Data

Attach Required Packages

AssayData-StdAssay

Get and Set Assay Data

Assay5-validity

V5 Assay Validity