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SeuratObject (version 4.0.1)

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) for more details.

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install.packages('SeuratObject')

Monthly Downloads

40,291

Version

4.0.1

License

GPL-3

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Last Published

May 8th, 2021

Functions in SeuratObject (4.0.1)

CellsByImage

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

Conditional Garbage Collection
AddMetaData

Add in metadata associated with either cells or features.
Cells

Get cells present in an object
Command

Get SeuratCommands
CellsByIdentities

Get cell names grouped by identity class
Assay-class

The Assay Class
Assay-methods

Assay Methods
AttachDeps

Attach Required Packages
AssayData

Get and Set Assay Data
CreateSeuratObject

Create a Seurat object
Embeddings

Get Cell Embeddings
Distances

Get the Neighbor nearest neighbors distance matrix
Idents

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

Get Neighbor algorithm index
JackStrawData-methods

JackStrawData Methods
DefaultAssay

Default Assay
Key

Get and set object keys
Indices

Get Neighbor nearest neighbor index matrices
GetImage

Get image data
FetchData

Access cellular data
CreateAssayObject

Create an Assay object
GetTissueCoordinates

Get tissue coordinates
Graph-class

The Graph Class
CreateDimReducObject

Create a DimReduc object
Misc

Get and set miscellaneous data
Seurat-methods

Seurat Methods
SeuratCommand-class

The SeuratCommand Class
IsMatrixEmpty

Check if a matrix is empty
IsGlobal

Is an object global/persistent?
DimReduc-methods

DimReduc Methods
DimReduc-class

The Dimensional Reduction Class
Neighbor-methods

Neighbor Methods
JS

Get and set JackStraw information
JackStrawData-class

The JackStrawData Class
Neighbor-class

The Neighbor class
Images

Pull spatial image names
as.Graph

Coerce to a Graph Object
Seurat-class

The Seurat Class
HVFInfo

Highly Variable Features
Project

Get and set project information
RenameAssays

Rename assays in a Seurat object
Loadings

Get and set feature loadings
set-if-null

Set a default value depending on if an object is NULL
RowMergeSparseMatrices

Merge Sparse Matrices by Row
Radius

Get the spot radius from an image
RenameCells

Rename cells
UpdateSeuratObject

Update old Seurat object to accommodate new features
Assays

Query Specific Object Types
SpatialImage-class

The SpatialImage class
LogSeuratCommand

Log a command
SeuratObject-package

SeuratObject: Data Structures for Single Cell Data
Version

Get Version Information
SpatialImage-methods

SpatialImage methods
Stdev

Get the standard deviations for an object
Tool

Get and set additional tool data
WhichCells

Identify cells matching certain criteria
as.Neighbor

Coerce to a Neighbor Object
as.Seurat

Coerce to a Seurat Object
as.sparse

Cast to Sparse
SeuratCommand-methods

SeuratCommand Methods
pbmc_small

A small example version of the PBMC dataset
seurat-class

The Seurat Class
reexports

Objects exported from other packages
s4list

S4/List Conversion