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SeuratObject (version 4.0.4)

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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Version

Install

install.packages('SeuratObject')

Monthly Downloads

49,038

Version

4.0.4

License

MIT + file LICENSE

Issues

45

Pull Requests

4

Stars

27

Forks

30

Maintainer

Paul Hoffman

Last Published

November 23rd, 2021

Functions in SeuratObject (4.0.4)

CellsByIdentities

Get cell names grouped by identity class
Cells

Get cells present in an object
AssayData

Get and Set Assay Data
Assay-methods

Assay Methods
AttachDeps

Attach Required Packages
AddMetaData

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

The Assay Class
CellsByImage

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

Check the Use of Dots
CheckGC

Conditional Garbage Collection
DefaultDimReduc

Find the default DimReduc
FetchData

Access cellular data
Command

Get SeuratCommands
RenameCells

Rename cells
CheckMatrix

Check Matrix Validity
RenameAssays

Rename assays in a Seurat object
Embeddings

Get Cell Embeddings
GetImage

Get image data
DimReduc-class

The Dimensional Reduction Class
FilterObjects

Find Sub-objects of a Certain Class
CreateAssayObject

Create an Assay object
DimReduc-methods

DimReduc Methods
Distances

Get the Neighbor nearest neighbors distance matrix
CreateDimReducObject

Create a DimReduc object
Seurat-methods

Seurat Methods
Images

Pull spatial image names
JackStrawData-class

The JackStrawData Class
RandomName

Generate a random name
Idents

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

Get and set JackStraw information
Radius

Get the spot radius from an image
Loadings

Get and set feature loadings
LogSeuratCommand

Log a command
SeuratCommand-class

The SeuratCommand Class
Index

Get Neighbor algorithm index
as.Graph

Coerce to a Graph Object
Seurat-class

The Seurat Class
SpatialImage-methods

SpatialImage methods
Key

Get and set object keys
JackStrawData-methods

JackStrawData Methods
RowMergeSparseMatrices

Merge Sparse Matrices by Row
as.sparse

Cast to Sparse
as.Seurat

Coerce to a Seurat Object
set-if-null

Set a default value depending on if an object is NULL
SpatialImage-class

The SpatialImage class
PackageCheck

Check the existence of a package
SeuratObject-package

SeuratObject: Data Structures for Single Cell Data
SeuratCommand-methods

SeuratCommand Methods
IsGlobal

Is an object global/persistent?
Indices

Get Neighbor nearest neighbor index matrices
IsMatrixEmpty

Check if a matrix is empty
Project

Get and set project information
as.Neighbor

Coerce to a Neighbor Object
Stdev

Get the standard deviations for an object
Tool

Get and set additional tool data
CreateSeuratObject

Create a Seurat object
s4list

S4/List Conversion
Assays

Query Specific Object Types
reexports

Objects exported from other packages
Neighbor-methods

Neighbor Methods
Version

Get Version Information
DefaultAssay

Default Assay
Graph-class

The Graph Class
Neighbor-class

The Neighbor class
HVFInfo

Highly Variable Features
Misc

Get and set miscellaneous data
seurat-class

The Seurat Class
GetTissueCoordinates

Get tissue coordinates
UpdateSeuratObject

Update old Seurat object to accommodate new features
pbmc_small

A small example version of the PBMC dataset
WhichCells

Identify cells matching certain criteria