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SeuratObject (version 5.0.1)

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

44,052

Version

5.0.1

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

November 17th, 2023

Functions in SeuratObject (5.0.1)

Centroids-class

The Centroids Class

Centroids-methods

Centroids Methods

Get SeuratCommands

CheckLayersName

Check layers names for the input list

GetTissueCoordinates

Get tissue coordinates

Crop Coordinates

Get and Set the Default FOV

CreateDimReducObject

Create a DimReduc object

CreateCentroids

Create a Centroids Objects

Generate a Class Key

DefaultLayer-StdAssay

DimReduc-validity

Dimensional Reduction Validity

DefaultAssay-StdAssay

Cell and Feature Names

Cast Assay Layers

CreateAssay5Object

Create a v5 Assay object

Overlay Spatial Objects Over One Another

Get Cell Embeddings

Create Spatial Coordinates

CreateAssayObject

Create an Assay object

The Field of View Object

Is an object global/persistent?

Segmentation-class

The Segmentation Class

Extract delimiter information from a string.

Check if a matrix is empty

Check the Use of Dots

Is a Matrix Sparse

Check Matrix Validity

The Graph Class

JackStrawData-class

The JackStrawData Class

Get and set feature loadings

Get and set JackStraw information

Pull spatial image names

CellsByIdentities

Get cell names grouped by identity class

CheckFeaturesNames

Check features names format

Cell and Feature Names

Check the existence of a package

Conditional Garbage Collection

Stitch Matrices Together

Save and Load Seurat Objects from Rds files

Polygon Vertices

LogSeuratCommand

Empty Data Frames

Radian/Degree Conversions

CreateMolecules

Create a Molecules Object

The Dimensional Reduction Class

Rename assays in a Seurat object

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

Seurat-validity

Seurat Object Validity

dimnames.Assay5

Assay-Level Feature and Cell Names

Get and set object keys

CreateSegmentation

Create a Segmentation Objects

RegisterSparseMatrix

Register Sparse Matrix Classes

Query and Manipulate Assay Layers

CreateSeuratObject

Create a Seurat object

Get Neighbor nearest neighbor index matrices

Layers-StdAssay

Query and Manipulate Assay Layers

Get and set miscellaneous data

Core Assay Infrastructure

Get and set miscellaneous data

A Mixin for Keyed objects

LogMap-validity

Logical Map Validity

Access cellular data

Split and Join Layers Together

Get the offset angle

Feature and Cell Numbers

DefaultDimReduc

Find the default DimReduc

Segmentation-methods

Segmentation Methods

Get the Subobject Names

Query Specific Object Types

RenameCells-StdAssay

Neighbor-methods

Neighbor Methods

Simplify Geometry

Find Sub-objects of a Certain Class

Get the Neighbor nearest neighbors distance matrix

Get the standard deviations for an object

.DollarNames.SeuratCommand

Dollar-sign Autocompletion

S4/List Conversion

Get and Set Additional Tool Data

SeuratCommand-class

The SeuratCommand Class

Dimensional Reduction Meta-Information

SparseEmptyMatrix

Generate empty dgC sparse matrix

Get Neighbor algorithm index

Molecules-class

The Spatial Molecules Class

Generate a random name

The Neighbor class

JackStrawData-methods

JackStrawData Methods

as.matrix.LogMap

Coerce Logical Maps to Matrices

Convert Segmentation Layers

Identify cells matching certain criteria

SeuratObject-options

Check List Names

SeuratObject-package

SeuratObject: Data Structures for Single Cell Data

Aggregate Molecules into an Expression Matrix

Feature-Level Meta Data

Assay-Level Feature and Cell Names

UpdateSeuratObject

Update old Seurat object to accommodate new features

Coerce to a Graph Object

Find Subobjects Of A Certain Class

Assay Class Label

Highly Variable Features

Get Version Information

Get Parent S4 Classes

droplevels.LogMap

Drop Unused Logical Map Values

v5-assay-summaries

V5 Assay Summaries

Find A Subobject

Coerce to a Neighbor Object

Feature and Cell Numbers

.SelectFeatures

Combine and Select Features

Feature and Cell Numbers

Disk Loading Function

Get and set project information

Molecules-methods

Molecules Methods

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

SpatialImage-methods

SpatialImage methods

Update slots in an object

dimnames.StdAssay

Assay-Level Feature and Cell Names

Feature-Level Meta Data

Calculate nCount and nFeature

[[,LogMap,integer,missing-method

LogMap Interaction Methods

Get the spot radius from an image

StdAssay-validity

V5 Assay Validity

Feature-Level Meta Data

The Seurat Class

Identify Object Collections

BPCells Matrix Mode

Objects exported from other packages

.IsFutureSeurat

Test Future Compatibility with Seurat

.DollarNames.Assay

Dollar-sign Autocompletion

colMeans,Assay-method

Row and Column Sums and Means

dimnames.Seurat

Feature and Cell Names

Check Feature Margin

RowMergeSparseMatrices

Merge Sparse Matrices by Row

.CreateStdAssay

Generic Assay Creation

Subset an Assay

Identify Sparse Slots

SpatialImage-class

The SpatialImage class

$.SeuratCommand

Command Log Parameter Access

Coerce to a Seurat Object

Cell-Level Meta Data

VariableFeatures-StdAssay

Highly Variable Features

Find Observations by Value

Matrix-like Subsetting for Logical Maps

intersect.LogMap

Find Common Logical Map Values

Set If or If Not NA

.DollarNames.Assay5

Dollar-sign Autocompletion

.DollarNames.StdAssay

Dollar-sign Autocompletion

show,Graph-method

Graph Object Overview

Get the Margin of an Object

Propagate a List

as.list.SeuratCommand

Coerce a SeuratCommand to a list

Generate a Random Key

Get the Package that Defines a Class

Feature and Cell Numbers

show,LogMap-method

LogMap Object Overview

colMeans,Seurat-method

Row and Column Sums and Means

Original double-bracket assign

The Seurat Class

show,Assay-method

V3 Assay Overview

A small example version of the PBMC dataset

.DollarNames.Seurat

Dollar-sign Autocompletion

Regex Pattern for Keys

Find the Default FOV

show,seurat-method

Old Seurat Object Overview

[[<-,Seurat,NULL

Remove Subobjects and Cell-Level Meta Data

show,StdAssay-method

V5 Assay Overview

Set If or If Not NULL

Get Feature Loadings

[.SeuratCommand

Command Log Data Access

Print Top Feature Loadings

show,DimReduc-method

Dimensional Reduction Overview

Subobject Names

Merge Dimensional Reductions

Deprecate Functions and Arguments

Get Cell Embeddings

Merge Seurat Objects

Find a File Path

Move Files and Directories

show,SeuratCommand-method

Command Log Overview

Subobjects and Cell-Level Meta Data

show,Seurat-method

Seurat Object Overview

Subset Seurat Objects

Subset an Assay

subset.DimReduc

Subset a Dimensional Reduction

subset.StdAssay

Subset an Assay

Get and Set Assay Data

AddMetaData-StdAssay

Add in metadata associated with either cells or features.

The v5 Assay Object

Attach Required Packages

Add in metadata associated with either cells or features.

The Assay Class

Assay5-validity

V5 Assay Validity

V3 Assay Validity

Get, Set, and Query Segmentation Boundaries

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

AssayData-StdAssay

Get and Set Assay Data

The Transposed v5 Assay Object

CastAssay-StdAssay

Cast Assay Layers