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SeuratObject (version 4.0.2)

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) for more details.

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install.packages('SeuratObject')

Monthly Downloads

43,228

Version

4.0.2

License

GPL-3

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Maintainer

Paul Hoffman

Last Published

June 9th, 2021

Functions in SeuratObject (4.0.2)

Command

Get SeuratCommands
Assay-class

The Assay Class
CellsByImage

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

Add in metadata associated with either cells or features.
Assay-methods

Assay Methods
AttachDeps

Attach Required Packages
Cells

Get cells present in an object
CellsByIdentities

Get cell names grouped by identity class
CheckGC

Conditional Garbage Collection
AssayData

Get and Set Assay Data
Distances

Get the Neighbor nearest neighbors distance matrix
GetImage

Get image data
FetchData

Access cellular data
JS

Get and set JackStraw information
DimReduc-methods

DimReduc Methods
Key

Get and set object keys
Graph-class

The Graph Class
DimReduc-class

The Dimensional Reduction Class
JackStrawData-methods

JackStrawData Methods
GetTissueCoordinates

Get tissue coordinates
Idents

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

Get the spot radius from an image
Project

Get and set project information
Images

Pull spatial image names
JackStrawData-class

The JackStrawData Class
Loadings

Get and set feature loadings
Index

Get Neighbor algorithm index
Embeddings

Get Cell Embeddings
Indices

Get Neighbor nearest neighbor index matrices
LogSeuratCommand

Log a command
SpatialImage-methods

SpatialImage methods
SpatialImage-class

The SpatialImage class
CreateAssayObject

Create an Assay object
CreateDimReducObject

Create a DimReduc object
Neighbor-class

The Neighbor class
Misc

Get and set miscellaneous data
RenameAssays

Rename assays in a Seurat object
RenameCells

Rename cells
IsMatrixEmpty

Check if a matrix is empty
DefaultAssay

Default Assay
IsGlobal

Is an object global/persistent?
Neighbor-methods

Neighbor Methods
CreateSeuratObject

Create a Seurat object
RowMergeSparseMatrices

Merge Sparse Matrices by Row
Assays

Query Specific Object Types
Seurat-methods

Seurat Methods
SeuratCommand-methods

SeuratCommand Methods
UpdateSeuratObject

Update old Seurat object to accommodate new features
Seurat-class

The Seurat Class
HVFInfo

Highly Variable Features
as.sparse

Cast to Sparse
as.Seurat

Coerce to a Seurat Object
SeuratCommand-class

The SeuratCommand Class
s4list

S4/List Conversion
WhichCells

Identify cells matching certain criteria
Version

Get Version Information
reexports

Objects exported from other packages
as.Neighbor

Coerce to a Neighbor Object
as.Graph

Coerce to a Graph Object
Tool

Get and set additional tool data
Stdev

Get the standard deviations for an object
seurat-class

The Seurat Class
set-if-null

Set a default value depending on if an object is NULL
SeuratObject-package

SeuratObject: Data Structures for Single Cell Data
pbmc_small

A small example version of the PBMC dataset