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SeuratObject (version 5.0.2)

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) , Hao Y, Hao S, et al (2021) and Hao Y, et al (2023) for more details.

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Install

install.packages('SeuratObject')

Monthly Downloads

45,294

Version

5.0.2

License

MIT + file LICENSE

Issues

39

Pull Requests

9

Stars

24

Forks

25

Maintainer

Paul Hoffman

Last Published

May 8th, 2024

Functions in SeuratObject (5.0.2)

Cells

Cell and Feature Names
Centroids-methods

Centroids Methods
CheckDots

Check the Use of Dots
CellsByImage

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

Get, Set, and Query Segmentation Boundaries
CellsByIdentities

Get cell names grouped by identity class
CastAssay

Cast Assay Layers
Centroids-class

The Centroids Class
CheckLayersName

Check layers names for the input list
Cells-StdAssay

Cell and Feature Names
CastAssay-StdAssay

Cast Assay Layers
CreateAssayObject

Create an Assay object
CreateAssay5Object

Create a v5 Assay object
CheckFeaturesNames

Check features names format
Command

Get SeuratCommands
Crop

Crop Coordinates
DefaultAssay-StdAssay

Default Assay
ClassKey

Generate a Class Key
CreateSeuratObject

Create a Seurat object
CreateSegmentation

Create a Segmentation Objects
CheckGC

Conditional Garbage Collection
Distances

Get the Neighbor nearest neighbors distance matrix
CheckMatrix

Check Matrix Validity
DimReduc-validity

Dimensional Reduction Validity
DefaultAssay

Default Assay
DefaultDimReduc

Find the default DimReduc
EmptyMatrix

Empty Matrices
CreateMolecules

Create a Molecules Object
CreateFOV

Create Spatial Coordinates
DefaultLayer

Default Layer
Embeddings

Get Cell Embeddings
DimReduc-class

The Dimensional Reduction Class
ExtractField

Extract delimiter information from a string.
Idents

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

Pull spatial image names
GetTissueCoordinates

Get tissue coordinates
Graph-class

The Graph Class
FOV-class

The Field of View Object
JackStrawData-class

The JackStrawData Class
JackStrawData-methods

JackStrawData Methods
KeyMixin-class

A Mixin for Keyed objects
CreateCentroids

Create a Centroids Objects
DefaultFOV

Get and Set the Default FOV
CreateDimReducObject

Create a DimReduc object
DefaultLayer-StdAssay

Default Layer
IsGlobal

Is an object global/persistent?
Indices

Get Neighbor nearest neighbor index matrices
FOV-methods

FOV Methods
IsSparse

Is a Matrix Sparse
JS

Get and set JackStraw information
GetImage

Get image data
FilterObjects

Find Sub-objects of a Certain Class
EmptyDF

Empty Data Frames
LogSeuratCommand

Log a command
Overlay

Overlay Spatial Objects Over One Another
PackageCheck

Check the existence of a package
Neighbor-methods

Neighbor Methods
LayerData

Query and Manipulate Assay Layers
Misc

Get and set miscellaneous data
IsNamedList

Check List Names
Molecules-methods

Molecules Methods
Layers-StdAssay

Query and Manipulate Assay Layers
IsMatrixEmpty

Check if a matrix is empty
Molecules-class

The Spatial Molecules Class
Assays

Query Specific Object Types
Segmentation-class

The Segmentation Class
Key

Get and set object keys
FOV-validity

FOV Validity
RenameCells

Rename cells
Misc-StdAssay

Get and set miscellaneous data
RenameCells-StdAssay

Rename cells
LogMap-validity

Logical Map Validity
Index

Get Neighbor algorithm index
LogMap

A Logical Map
FetchData

Access cellular data
SaveSeuratRds

Save and Load Seurat Objects from Rds files
Loadings

Get and set feature loadings
RowMergeSparseMatrices

Merge Sparse Matrices by Row
Key-validity

Key Validity
Simplify

Simplify Geometry
Segmentation-methods

Segmentation Methods
Neighbor-class

The Neighbor class
SeuratObject-package

SeuratObject: Data Structures for Single Cell Data
Seurat-class

The Seurat Class
SeuratCommand-class

The SeuratCommand Class
SeuratObject-options

Seurat Options
UpdateSeuratObject

Update old Seurat object to accommodate new features
MatchCells

Match Cells
UpdateSlots

Update slots in an object
VariableFeatures-StdAssay

Highly Variable Features
HVFInfo

Highly Variable Features
SpatialImage-class

The SpatialImage class
as.Centroids

Convert Segmentation Layers
SparseEmptyMatrix

Generate empty dgC sparse matrix
Angles

Radian/Degree Conversions
aggregate

Aggregate Molecules into an Expression Matrix
JoinLayers

Split and Join Layers Together
Project

Get and set project information
SpatialImage-methods

SpatialImage methods
RenameAssays

Rename assays in a Seurat object
Tool

Get and Set Additional Tool Data
PolyVtx

Polygon Vertices
Theta

Get the offset angle
RegisterSparseMatrix

Register Sparse Matrix Classes
Radius

Get the spot radius from an image
as.Seurat

Coerce to a Seurat Object
as.Neighbor

Coerce to a Neighbor Object
$.SeuratCommand

Command Log Parameter Access
Seurat-validity

Seurat Object Validity
$.StdAssay

Layer Data
RandomName

Generate a random name
dimnames.StdAssay

Assay-Level Feature and Cell Names
StdAssay-validity

V5 Assay Validity
StdAssay-class

Core Assay Infrastructure
Stdev

Get the standard deviations for an object
as.sparse

Cast to Sparse
$.Assay

Layer Data
$.Seurat

Cell-Level Meta Data
$.Assay5

Layer Data
WhichCells

Identify cells matching certain criteria
Version

Get Version Information
colMeans,Assay-method

Row and Column Sums and Means
dimnames.Seurat

Feature and Cell Names
dimnames.Assay5

Assay-Level Feature and Cell Names
dimnames.Assay

Assay-Level Feature and Cell Names
StitchMatrix

Stitch Matrices Together
.DollarNames.SeuratCommand

Dollar-sign Autocompletion
as.matrix.LogMap

Coerce Logical Maps to Matrices
.Collections

Identify Object Collections
.FilePath

Find a File Path
colMeans,Seurat-method

Row and Column Sums and Means
.FilterObjects

Find Subobjects Of A Certain Class
dim.StdAssay

Feature and Cell Numbers
.DollarNames.Seurat

Dollar-sign Autocompletion
.Contains

Get Parent S4 Classes
as.list.SeuratCommand

Coerce a SeuratCommand to a list
as.Graph

Coerce to a Graph Object
dim.Assay

Feature and Cell Numbers
.Deprecate

Deprecate Functions and Arguments
.AssayClass

Assay Class Label
dim.Seurat

Feature and Cell Numbers
dim.DimReduc

Dimensional Reduction Meta-Information
dim.Assay5

Feature and Cell Numbers
.IsFutureSeurat

Test Future Compatibility with Seurat
.DiskLoad

Disk Loading Function
.ClassPkg

Get the Package that Defines a Class
.DefaultFOV

Find the Default FOV
.CheckFmargin

Check Feature Margin
.CreateStdAssay

Generic Assay Creation
.KeyPattern

Regex Pattern for Keys
.RandomKey

Generate a Random Key
seurat-class

The Seurat Class
.DollarNames.StdAssay

Dollar-sign Autocompletion
labels.LogMap

Find Observations by Value
merge.DimReduc

Merge Dimensional Reductions
names.Seurat

Subobject Names
merge.Seurat

Merge Seurat Objects
merge.Assay5

Merge Assays
.DollarNames.Assay

Dollar-sign Autocompletion
.BPMatrixMode

BPCells Matrix Mode
.GetMethod

Get a Method
.CalcN

Calculate nCount and nFeature
.FindObject

Find A Subobject
.SelectFeatures

Combine and Select Features
[.SeuratCommand

Command Log Data Access
.DollarNames.Assay5

Dollar-sign Autocompletion
[.StdAssay

Layer Data
show,seurat-method

Old Seurat Object Overview
merge.StdAssay

Merge Assays
.MARGIN

Get the Margin of an Object
split.Assay

Split an Assay
merge.Assay

Merge Assays
.PropagateList

Propagate a List
.SparseSlots

Identify Sparse Slots
s4list

S4/List Conversion
[[.DimReduc

Get Cell Embeddings
[[.Assay5

Feature-Level Meta Data
.Subobjects

Get the Subobject Names
print.DimReduc

Print Top Feature Loadings
.FileMove

Move Files and Directories
intersect.LogMap

Find Common Logical Map Values
droplevels.LogMap

Drop Unused Logical Map Values
show,LogMap-method

LogMap Object Overview
[[.Seurat

Subobjects and Cell-Level Meta Data
show,Seurat-method

Seurat Object Overview
set-if-null

Set If or If Not NULL
old-assign

Original double-bracket assign
pbmc_small

A small example version of the PBMC dataset
[.Assay

Layer Data
split.StdAssay

Split an Assay
[[,LogMap,integer,missing-method

LogMap Interaction Methods
v5-assay-summaries

V5 Assay Summaries
[[<-,Seurat,NULL

Remove Subobjects and Cell-Level Meta Data
subset.StdAssay

Subset an Assay
split.Assay5

Split an Assay
show,SeuratCommand-method

Command Log Overview
split.Seurat

Split an Assay
reexports

Objects exported from other packages
show,Assay-method

V3 Assay Overview
[.DimReduc

Get Feature Loadings
[.Assay5

Layer Data
subset.DimReduc

Subset a Dimensional Reduction
[[<-,Seurat

Add Subobjects
[[.StdAssay

Feature-Level Meta Data
[,LogMap

Matrix-like Subsetting for Logical Maps
show,DimReduc-method

Dimensional Reduction Overview
[[.Assay

Feature-Level Meta Data
show,StdAssay-method

V5 Assay Overview
subset.Seurat

Subset Seurat Objects
subset.Assay5

Subset an Assay
subset.Assay

Subset an Assay
set-if-na

Set If or If Not NA
[[<-,Seurat,character,missing,StdAssay-method

Add Subobjects
show,Graph-method

Graph Object Overview
AddMetaData

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

V3 Assay Validity
Assay-class

The Assay Class
AddMetaData-StdAssay

Add in metadata associated with either cells or features.
Assay5-class

The v5 Assay Object
Assay5T-class

The Transposed v5 Assay Object
AssayData

Get and Set Assay Data
AttachDeps

Attach Required Packages
AssayData-StdAssay

Get and Set Assay Data
Assay5-validity

V5 Assay Validity