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SeuratObject (version 4.1.0)

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

36,554

Version

4.1.0

License

MIT + file LICENSE

Issues

44

Pull Requests

13

Stars

25

Forks

29

Maintainer

Paul Hoffman

Last Published

May 1st, 2022

Functions in SeuratObject (4.1.0)

AddMetaData

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

The Assay Class
CellsByIdentities

Get cell names grouped by identity class
AssayData

Get and Set Assay Data
Angles

Radian/Degree Conversions
Boundaries

Get, Set, and Query Segmentation Boundaries
CellsByImage

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

Assay Methods
AttachDeps

Attach Required Packages
CheckDots

Check the Use of Dots
CheckGC

Conditional Garbage Collection
DefaultDimReduc

Find the default DimReduc
Embeddings

Get Cell Embeddings
DefaultAssay

Default Assay
Cells

Cell and Feature Names
CreateCentroids

Create a Centroids Objects
CreateAssayObject

Create an Assay object
CreateDimReducObject

Create a DimReduc object
CreateFOV

Create Spatial Coordinates
CheckMatrix

Check Matrix Validity
DimReduc-methods

DimReduc Methods
CreateMolecules

Create a Molecules Object
EmptyDF

Empty Data Frames
FOV-class

The Field of View Object
Command

Get SeuratCommands
Distances

Get the Neighbor nearest neighbors distance matrix
FetchData

Access cellular data
CreateSegmentation

Create a Segmentation Objects
Centroids-class

The Centroids Class
Key

Get and set object keys
LogSeuratCommand

Log a command
LogMap-class

A Logical Map
JackStrawData-methods

JackStrawData Methods
RandomName

Generate a random name
RenameAssays

Rename assays in a Seurat object
FOV-methods

FOV Methods
KeyMixin-class

A Mixin for Keyed objects
SeuratCommand-class

The SeuratCommand Class
Centroids-methods

Centroids Methods
SpatialImage-methods

SpatialImage methods
Neighbor-class

The Neighbor class
JS

Get and set JackStraw information
as.Graph

Coerce to a Graph Object
Neighbor-methods

Neighbor Methods
FilterObjects

Find Sub-objects of a Certain Class
JackStrawData-class

The JackStrawData Class
SpatialImage-class

The SpatialImage class
DefaultFOV

Get and Set the Default FOV
DimReduc-class

The Dimensional Reduction Class
Idents

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

Is an object global/persistent?
Graph-class

The Graph Class
Indices

Get Neighbor nearest neighbor index matrices
CreateSeuratObject

Create a Seurat object
Crop

Crop Coordinates
MatchCells

Match Cells
set-if-na

Set if NA
as.Neighbor

Coerce to a Neighbor Object
set-if-null

Set a default value depending on if an object is NULL
SeuratCommand-methods

SeuratCommand Methods
RenameCells

Rename cells
Version

Get Version Information
Seurat-class

The Seurat Class
Misc

Get and set miscellaneous data
RowMergeSparseMatrices

Merge Sparse Matrices by Row
Seurat-methods

Seurat Methods
Index

Get Neighbor algorithm index
Images

Pull spatial image names
Molecules-class

The Spatial Molecules Class
Loadings

Get and set feature loadings
Molecules-methods

Molecules Methods
GetTissueCoordinates

Get tissue coordinates
IsNamedList

Check List Names
Segmentation-methods

Segmentation Methods
Overlay

Overlay Spatial Objects Over One Another
GetImage

Get image data
Assays

Query Specific Object Types
IsMatrixEmpty

Check if a matrix is empty
Segmentation-class

The Segmentation Class
Stdev

Get the standard deviations for an object
Project

Get and set project information
Radius

Get the spot radius from an image
PolyVtx

Polygon Vertices
PackageCheck

Check the existence of a package
Theta

Get the offset angle
UpdateSlots

Update slots in an object
HVFInfo

Highly Variable Features
reexports

Objects exported from other packages
s4list

S4/List Conversion
seurat-class

The Seurat Class
pbmc_small

A small example version of the PBMC dataset
aggregate

Aggregate Molecules into an Expression Matrix
SeuratObject-package

SeuratObject: Data Structures for Single Cell Data
WhichCells

Identify cells matching certain criteria
as.Centroids

Convert Segmentation Layers
as.sparse

Cast to Sparse
as.Seurat

Coerce to a Seurat Object
Simplify

Simplify Geometry
Tool

Get and set additional tool data
UpdateSeuratObject

Update old Seurat object to accommodate new features
.Contains

Get Parent S4 Classes
.DefaultFOV

Find the Default FOV