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SeuratObject (version 4.1.4)

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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Install

install.packages('SeuratObject')

Monthly Downloads

40,291

Version

4.1.4

License

MIT + file LICENSE

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Last Published

September 26th, 2023

Functions in SeuratObject (4.1.4)

CheckDots

Check the Use of Dots
CheckGC

Conditional Garbage Collection
Centroids-class

The Centroids Class
Centroids-methods

Centroids Methods
Crop

Crop Coordinates
CreateSeuratObject

Create a Seurat object
Command

Get SeuratCommands
DimReduc-methods

DimReduc Methods
CheckMatrix

Check Matrix Validity
Distances

Get the Neighbor nearest neighbors distance matrix
CreateDimReducObject

Create a DimReduc object
DefaultFOV

Get and Set the Default FOV
CreateAssayObject

Create an Assay object
CreateFOV

Create Spatial Coordinates
Embeddings

Get Cell Embeddings
Graph-class

The Graph Class
EmptyDF

Empty Data Frames
DefaultAssay

Default Assay
CreateCentroids

Create a Centroids Objects
CreateMolecules

Create a Molecules Object
DimReduc-class

The Dimensional Reduction Class
Idents

Get, set, and manipulate an object's identity classes
FOV-methods

FOV Methods
FOV-class

The Field of View Object
IsNamedList

Check List Names
FilterObjects

Find Sub-objects of a Certain Class
DefaultDimReduc

Find the default DimReduc
FetchData

Access cellular data
Images

Pull spatial image names
IsGlobal

Is an object global/persistent?
IsMatrixEmpty

Check if a matrix is empty
Loadings

Get and set feature loadings
LogMap-class

A Logical Map
GetImage

Get image data
CreateSegmentation

Create a Segmentation Objects
JS

Get and set JackStraw information
GetTissueCoordinates

Get tissue coordinates
RandomName

Generate a random name
Indices

Get Neighbor nearest neighbor index matrices
RenameAssays

Rename assays in a Seurat object
JackStrawData-methods

JackStrawData Methods
JackStrawData-class

The JackStrawData Class
Neighbor-class

The Neighbor class
Misc

Get and set miscellaneous data
Key

Get and set object keys
Molecules-methods

Molecules Methods
Neighbor-methods

Neighbor Methods
KeyMixin-class

A Mixin for Keyed objects
LogSeuratCommand

Log a command
MatchCells

Match Cells
Radius

Get the spot radius from an image
Molecules-class

The Spatial Molecules Class
Project

Get and set project information
Index

Get Neighbor algorithm index
SpatialImage-class

The SpatialImage class
SpatialImage-methods

SpatialImage methods
Seurat-class

The Seurat Class
RenameCells

Rename cells
RowMergeSparseMatrices

Merge Sparse Matrices by Row
Seurat-methods

Seurat Methods
Tool

Get and set additional tool data
SeuratObject-package

SeuratObject: Data Structures for Single Cell Data
Assays

Query Specific Object Types
Overlay

Overlay Spatial Objects Over One Another
Version

Get Version Information
WhichCells

Identify cells matching certain criteria
PolyVtx

Polygon Vertices
SeuratCommand-methods

SeuratCommand Methods
as.Centroids

Convert Segmentation Layers
Segmentation-class

The Segmentation Class
as.Neighbor

Coerce to a Neighbor Object
PackageCheck

Check the existence of a package
aggregate

Aggregate Molecules into an Expression Matrix
SeuratCommand-class

The SeuratCommand Class
as.Graph

Coerce to a Graph Object
Theta

Get the offset angle
.DefaultFOV

Find the Default FOV
Segmentation-methods

Segmentation Methods
Stdev

Get the standard deviations for an object
UpdateSeuratObject

Update old Seurat object to accommodate new features
as.Seurat

Coerce to a Seurat Object
s4list

S4/List Conversion
.Contains

Get Parent S4 Classes
reexports

Objects exported from other packages
as.sparse

Cast to Sparse
Simplify

Simplify Geometry
set-if-na

Set if NA
set-if-null

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

The Seurat Class
HVFInfo

Highly Variable Features
UpdateSlots

Update slots in an object
pbmc_small

A small example version of the PBMC dataset
CellsByImage

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

Assay Methods
AttachDeps

Attach Required Packages
Boundaries

Get, Set, and Query Segmentation Boundaries
Assay-class

The Assay Class
CellsByIdentities

Get cell names grouped by identity class
AddMetaData

Add in metadata associated with either cells or features.
AssayData

Get and Set Assay Data
Cells

Cell and Feature Names
Angles

Radian/Degree Conversions