Learn R Programming

⚠️There's a newer version (5.0.2) of this package.Take me there.

SeuratObject (version 5.0.0)

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

49,038

Version

5.0.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Paul Hoffman

Last Published

October 26th, 2023

Functions in SeuratObject (5.0.0)

The Assay Class

The v5 Assay Object

Cast Assay Layers

Attach Required Packages

Assay5-validity

V5 Assay Validity

Cell and Feature Names

Add in metadata associated with either cells or features.

The Transposed v5 Assay Object

Cell and Feature Names

AssayData-StdAssay

Get and Set Assay Data

Centroids-methods

Centroids Methods

Get, Set, and Query Segmentation Boundaries

CastAssay-StdAssay

Cast Assay Layers

CellsByIdentities

Get cell names grouped by identity class

CheckLayersName

Check layers names for the input list

Check Matrix Validity

Generate a Class Key

V3 Assay Validity

Check the Use of Dots

CheckFeaturesNames

Check features names format

Conditional Garbage Collection

CreateAssay5Object

Create a v5 Assay object

DefaultDimReduc

Find the default DimReduc

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

Get Cell Embeddings

Centroids-class

The Centroids Class

CreateAssayObject

Create an Assay object

Pull spatial image names

CreateCentroids

Create a Centroids Objects

Create Spatial Coordinates

CreateSegmentation

Create a Segmentation Objects

Empty Data Frames

Get Neighbor nearest neighbor index matrices

Layers-StdAssay

Query and Manipulate Assay Layers

CreateMolecules

Create a Molecules Object

CreateSeuratObject

Create a Seurat object

Query and Manipulate Assay Layers

Check the existence of a package

Get SeuratCommands

GetTissueCoordinates

Get tissue coordinates

CreateDimReducObject

Create a DimReduc object

Polygon Vertices

The Dimensional Reduction Class

Get and set JackStraw information

Get and Set Additional Tool Data

Get and set object keys

Crop Coordinates

DefaultAssay-StdAssay

Get and Set the Default FOV

DefaultLayer-StdAssay

A Mixin for Keyed objects

Extract delimiter information from a string.

UpdateSeuratObject

Update old Seurat object to accommodate new features

The Field of View Object

Is an object global/persistent?

JackStrawData-class

The JackStrawData Class

Radian/Degree Conversions

DimReduc-validity

Dimensional Reduction Validity

Check if a matrix is empty

JackStrawData-methods

JackStrawData Methods

Convert Segmentation Layers

Get and set feature loadings

Feature and Cell Numbers

The Graph Class

Dimensional Reduction Meta-Information

Get and set miscellaneous data

Get Parent S4 Classes

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

Check List Names

Get the Neighbor nearest neighbors distance matrix

Access cellular data

.CreateStdAssay

Generic Assay Creation

.SelectFeatures

Combine and Select Features

Query Specific Object Types

RowMergeSparseMatrices

Merge Sparse Matrices by Row

Split and Join Layers Together

Overlay Spatial Objects Over One Another

Segmentation-methods

Segmentation Methods

Identify Sparse Slots

Find Sub-objects of a Certain Class

Core Assay Infrastructure

Is a Matrix Sparse

Get and set miscellaneous data

Identify cells matching certain criteria

The Seurat Class

Simplify Geometry

SparseEmptyMatrix

Generate empty dgC sparse matrix

Update slots in an object

VariableFeatures-StdAssay

Highly Variable Features

Molecules-methods

Molecules Methods

Aggregate Molecules into an Expression Matrix

Get the Package that Defines a Class

Coerce to a Graph Object

Get Neighbor algorithm index

The Neighbor class

Coerce to a Neighbor Object

Objects exported from other packages

Neighbor-methods

Neighbor Methods

Identify Object Collections

LogMap-validity

Logical Map Validity

LogSeuratCommand

Get and set project information

Rename assays in a Seurat object

Molecules-class

The Spatial Molecules Class

S4/List Conversion

colMeans,Assay-method

Row and Column Sums and Means

RenameCells-StdAssay

.DollarNames.Assay5

Dollar-sign Autocompletion

SeuratObject-options

Get the spot radius from an image

show,StdAssay-method

V5 Assay Overview

Generate a random name

RegisterSparseMatrix

Register Sparse Matrix Classes

.DollarNames.Seurat

Dollar-sign Autocompletion

Assay Class Label

Seurat-validity

Seurat Object Validity

SeuratCommand-class

The SeuratCommand Class

SeuratObject-package

SeuratObject: Data Structures for Single Cell Data

BPCells Matrix Mode

Find Subobjects Of A Certain Class

show,seurat-method

Old Seurat Object Overview

Find A Subobject

Regex Pattern for Keys

StdAssay-validity

V5 Assay Validity

Highly Variable Features

Get the standard deviations for an object

Save and Load Seurat Objects from Rds files

Get Version Information

Segmentation-class

The Segmentation Class

SpatialImage-class

The SpatialImage class

as.matrix.LogMap

Coerce Logical Maps to Matrices

Stitch Matrices Together

Get the Margin of an Object

Get Cell Embeddings

Subobject Names

show,Seurat-method

Seurat Object Overview

colMeans,Seurat-method

Row and Column Sums and Means

SpatialImage-methods

SpatialImage methods

Feature and Cell Numbers

Get the offset angle

dimnames.Seurat

Feature and Cell Names

Subobjects and Cell-Level Meta Data

A small example version of the PBMC dataset

Print Top Feature Loadings

dimnames.StdAssay

Assay-Level Feature and Cell Names

show,SeuratCommand-method

Command Log Overview

Coerce to a Seurat Object

Find the Default FOV

Feature-Level Meta Data

Get Feature Loadings

[[,LogMap,integer,missing-method

LogMap Interaction Methods

[.SeuratCommand

Command Log Data Access

Deprecate Functions and Arguments

as.list.SeuratCommand

Coerce a SeuratCommand to a list

Cell-Level Meta Data

$.SeuratCommand

Command Log Parameter Access

Subset Seurat Objects

Move Files and Directories

subset.StdAssay

Subset an Assay

Feature and Cell Numbers

Find a File Path

Calculate nCount and nFeature

Feature and Cell Numbers

Check Feature Margin

intersect.LogMap

Find Common Logical Map Values

Find Observations by Value

.DollarNames.SeuratCommand

Dollar-sign Autocompletion

.DollarNames.StdAssay

Dollar-sign Autocompletion

Propagate a List

Assay-Level Feature and Cell Names

dimnames.Assay5

Assay-Level Feature and Cell Names

Disk Loading Function

.DollarNames.Assay

Dollar-sign Autocompletion

Generate a Random Key

Get the Subobject Names

droplevels.LogMap

Drop Unused Logical Map Values

.IsFutureSeurat

Test Future Compatibility with Seurat

Set If or If Not NA

Set If or If Not NULL

Merge Dimensional Reductions

Subset an Assay

show,Assay-method

V3 Assay Overview

show,DimReduc-method

Dimensional Reduction Overview

subset.DimReduc

Subset a Dimensional Reduction

Merge Seurat Objects

Original double-bracket assign

show,Graph-method

Graph Object Overview

The Seurat Class

show,LogMap-method

LogMap Object Overview

Feature-Level Meta Data

Feature-Level Meta Data

Matrix-like Subsetting for Logical Maps

[[<-,Seurat,NULL

Remove Subobjects and Cell-Level Meta Data

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

Subset an Assay

v5-assay-summaries

V5 Assay Summaries

AddMetaData-StdAssay

Add in metadata associated with either cells or features.

Get and Set Assay Data