Data Structures for Single Cell Data

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Documentation for package ‘SeuratObject’ version 4.0.4

• DESCRIPTION file.

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A C D E F G H I J K L M N P R S T U V W misc

SeuratObject-package

SeuratObject: Data Structures for Single Cell Data

-- A --

AddMetaData	Add in metadata associated with either cells or features.
AddMetaData.Assay	Add in metadata associated with either cells or features.
AddMetaData.Seurat	Add in metadata associated with either cells or features.
AddSamples	Seurat Methods
as.Graph	Coerce to a 'Graph' Object
as.Graph.Matrix	Coerce to a 'Graph' Object
as.Graph.matrix	Coerce to a 'Graph' Object
as.Graph.Neighbor	Coerce to a 'Graph' Object
as.list.SeuratCommand	'SeuratCommand' Methods
as.logical.JackStrawData	'JackStrawData' Methods
as.Neighbor	Coerce to a 'Neighbor' Object
as.Neighbor.Graph	Coerce to a 'Neighbor' Object
as.Seurat	Coerce to a 'Seurat' Object
as.sparse	Cast to Sparse
as.sparse.data.frame	Cast to Sparse
as.sparse.Matrix	Cast to Sparse
as.sparse.matrix	Cast to Sparse
Assay	The Assay Class
Assay-class	The Assay Class
Assay-methods	'Assay' Methods
AssayData	Get and Set Assay Data
Assays	Query Specific Object Types
AttachDeps	Attach Required Packages

-- C --

Cells	Get cells present in an object
Cells.default	Get cells present in an object
Cells.DimReduc	Get cells present in an object
Cells.Neighbor	Get cells present in an object
Cells.SpatialImage	'SpatialImage' methods
CellsByIdentities	Get cell names grouped by identity class
CellsByImage	Get a vector of cell names associated with an image (or set of images)
CheckGC	Conditional Garbage Collection
colMeans-method	'Assay' Methods
colMeans-method	Seurat Methods
colSums-method	'Assay' Methods
colSums-method	Seurat Methods
Command	Get SeuratCommands
Command.Seurat	Get SeuratCommands
CreateAssayObject	Create an Assay object
CreateDimReducObject	Create a DimReduc object
CreateSeuratObject	Create a 'Seurat' object
CreateSeuratObject.Assay	Create a 'Seurat' object
CreateSeuratObject.default	Create a 'Seurat' object

-- D --

DefaultAssay	Default Assay
DefaultAssay.Assay	Default Assay
DefaultAssay.DimReduc	Default Assay
DefaultAssay.Graph	Default Assay
DefaultAssay.Seurat	Default Assay
DefaultAssay.SeuratCommand	Default Assay
DefaultAssay.SpatialImage	'SpatialImage' methods
DefaultAssay<-	Default Assay
DefaultAssay<-.Assay	Default Assay
DefaultAssay<-.DimReduc	Default Assay
DefaultAssay<-.Graph	Default Assay
DefaultAssay<-.Seurat	Default Assay
DefaultAssay<-.SpatialImage	'SpatialImage' methods
DefaultDimReduc	Find the default 'DimReduc'
dim.Assay	'Assay' Methods
dim.DimReduc	'DimReduc' Methods
dim.Neighbor	'Neighbor' Methods
dim.Seurat	Seurat Methods
dim.SpatialImage	'SpatialImage' methods
dimnames.Assay	'Assay' Methods
dimnames.DimReduc	'DimReduc' Methods
dimnames.Seurat	Seurat Methods
DimReduc	The Dimensional Reduction Class
DimReduc-class	The Dimensional Reduction Class
DimReduc-methods	'DimReduc' Methods
Distances	Get the Neighbor nearest neighbors distance matrix
Distances.Neighbor	Get the Neighbor nearest neighbors distance matrix
droplevels.Seurat	Get, set, and manipulate an object's identity classes

-- E --

Embeddings	Get Cell Embeddings
Embeddings.DimReduc	Get Cell Embeddings
Embeddings.Seurat	Get Cell Embeddings

-- F --

FetchData	Access cellular data
FilterObjects	Find Sub-objects of a Certain Class

-- G --

GetAssayData	Get and Set Assay Data
GetAssayData.Assay	Get and Set Assay Data
GetAssayData.Seurat	Get and Set Assay Data
GetImage	Get image data
GetImage.Seurat	Get image data
GetImage.SpatialImage	'SpatialImage' methods
GetTissueCoordinates	Get tissue coordinates
GetTissueCoordinates.Seurat	Get tissue coordinates
GetTissueCoordinates.SpatialImage	'SpatialImage' methods
Graph	The Graph Class
Graph-class	The Graph Class
Graphs	Query Specific Object Types

-- H --

head.Assay	'Assay' Methods
head.Seurat	Seurat Methods
HVFInfo	Highly Variable Features
HVFInfo.Assay	Highly Variable Features
HVFInfo.Seurat	Highly Variable Features

-- I --

Idents	Get, set, and manipulate an object's identity classes
Idents.Seurat	Get, set, and manipulate an object's identity classes
Idents<-	Get, set, and manipulate an object's identity classes
Idents<-.Seurat	Get, set, and manipulate an object's identity classes
Images	Pull spatial image names
Index	Get Neighbor algorithm index
Index.Neighbor	Get Neighbor algorithm index
Index<-	Get Neighbor algorithm index
Index<-.Neighbor	Get Neighbor algorithm index
Indices	Get Neighbor nearest neighbor index matrices
Indices.Neighbor	Get Neighbor nearest neighbor index matrices
IsGlobal	Is an object global/persistent?
IsGlobal.default	Is an object global/persistent?
IsGlobal.DimReduc	Is an object global/persistent?
IsGlobal.SpatialImage	'SpatialImage' methods
IsMatrixEmpty	Check if a matrix is empty
IsS4List	S4/List Conversion

-- J --

JackStrawData	The JackStrawData Class
JackStrawData-class	The JackStrawData Class
JackStrawData-methods	'JackStrawData' Methods
JS	Get and set JackStraw information
JS.DimReduc	Get and set JackStraw information
JS.JackStrawData	Get and set JackStraw information
JS<-	Get and set JackStraw information
JS<-.DimReduc	Get and set JackStraw information
JS<-.JackStrawData	Get and set JackStraw information

-- K --

Key	Get and set object keys
Key.Assay	Get and set object keys
Key.DimReduc	Get and set object keys
Key.Seurat	Get and set object keys
Key.SpatialImage	'SpatialImage' methods
Key<-	Get and set object keys
Key<-.Assay	Get and set object keys
Key<-.DimReduc	Get and set object keys
Key<-.SpatialImage	'SpatialImage' methods

-- L --

length.DimReduc	'DimReduc' Methods
levels.Seurat	Get, set, and manipulate an object's identity classes
levels<-.Seurat	Get, set, and manipulate an object's identity classes
ListToS4	S4/List Conversion
Loadings	Get and set feature loadings
Loadings.DimReduc	Get and set feature loadings
Loadings.Seurat	Get and set feature loadings
Loadings<-	Get and set feature loadings
Loadings<-.DimReduc	Get and set feature loadings
LogSeuratCommand	Log a command

-- M --

merge	Seurat Methods
merge.Assay	'Assay' Methods
merge.DimReduc	'DimReduc' Methods
merge.Seurat	Seurat Methods
MergeSeurat	Seurat Methods
Misc	Get and set miscellaneous data
Misc.Assay	Get and set miscellaneous data
Misc.DimReduc	Get and set miscellaneous data
Misc.Seurat	Get and set miscellaneous data
Misc<-	Get and set miscellaneous data
Misc<-.Assay	Get and set miscellaneous data
Misc<-.DimReduc	Get and set miscellaneous data
Misc<-.Seurat	Get and set miscellaneous data

-- N --

names.DimReduc	'DimReduc' Methods
names.Seurat	Seurat Methods
Neighbor	The Neighbor class
Neighbor-class	The Neighbor class
Neighbor-methods	'Neighbor' Methods
Neighbors	Query Specific Object Types

-- P --

PackageCheck	Check the existence of a package
pbmc_small	A small example version of the PBMC dataset
print	'DimReduc' Methods
print.DimReduc	'DimReduc' Methods
Project	Get and set project information
Project.Seurat	Get and set project information
Project<-	Get and set project information
Project<-.Seurat	Get and set project information

-- R --

Radius	Get the spot radius from an image
Radius.SpatialImage	'SpatialImage' methods
RandomName	Generate a random name
Reductions	Query Specific Object Types
RenameAssays	Rename assays in a 'Seurat' object
RenameCells	Rename cells
RenameCells.Assay	Rename cells
RenameCells.DimReduc	Rename cells
RenameCells.Neighbor	Rename cells
RenameCells.Seurat	Rename cells
RenameCells.SpatialImage	'SpatialImage' methods
RenameIdent	Get, set, and manipulate an object's identity classes
RenameIdents	Get, set, and manipulate an object's identity classes
RenameIdents.Seurat	Get, set, and manipulate an object's identity classes
ReorderIdent	Get, set, and manipulate an object's identity classes
ReorderIdent.Seurat	Get, set, and manipulate an object's identity classes
rowMeans-method	'Assay' Methods
rowMeans-method	Seurat Methods
RowMergeSparseMatrices	Merge Sparse Matrices by Row
rowSums-method	'Assay' Methods
rowSums-method	Seurat Methods

-- S --

s4list	S4/List Conversion
S4ToList	S4/List Conversion
S4ToList.default	S4/List Conversion
S4ToList.list	S4/List Conversion
SetAssayData	Get and Set Assay Data
SetAssayData.Assay	Get and Set Assay Data
SetAssayData.Seurat	Get and Set Assay Data
SetDimReduction	Create a DimReduc object
SetIdent	Get, set, and manipulate an object's identity classes
SetIdent.Seurat	Get, set, and manipulate an object's identity classes
Seurat	The Seurat Class
seurat	The Seurat Class
Seurat-class	The Seurat Class
seurat-class	The Seurat Class
Seurat-methods	Seurat Methods
SeuratAccess	Add in metadata associated with either cells or features.
SeuratCommand	The SeuratCommand Class
SeuratCommand-class	The SeuratCommand Class
SeuratCommand-methods	'SeuratCommand' Methods
SeuratObject	SeuratObject: Data Structures for Single Cell Data
show-method	'Assay' Methods
show-method	'DimReduc' Methods
show-method	'JackStrawData' Methods
show-method	'Neighbor' Methods
show-method	Seurat Methods
show-method	'SeuratCommand' Methods
show-method	'SpatialImage' methods
show-method	The Seurat Class
SpatialImage	The SpatialImage class
SpatialImage-class	The SpatialImage class
SpatialImage-methods	'SpatialImage' methods
SpatiallyVariableFeatures	Highly Variable Features
SpatiallyVariableFeatures.Assay	Highly Variable Features
SpatiallyVariableFeatures.Seurat	Highly Variable Features
StashIdent	Get, set, and manipulate an object's identity classes
StashIdent.Seurat	Get, set, and manipulate an object's identity classes
Stdev	Get the standard deviations for an object
Stdev.DimReduc	Get the standard deviations for an object
Stdev.Seurat	Get the standard deviations for an object
subset	Seurat Methods
subset.Assay	'Assay' Methods
subset.DimReduc	'DimReduc' Methods
subset.Seurat	Seurat Methods
subset.SpatialImage	'SpatialImage' methods
SVFInfo	Highly Variable Features
SVFInfo.Assay	Highly Variable Features
SVFInfo.Seurat	Highly Variable Features

-- T --

tail.Assay	'Assay' Methods
tail.Seurat	Seurat Methods
Tool	Get and set additional tool data
Tool.Seurat	Get and set additional tool data
Tool<-	Get and set additional tool data
Tool<-.Seurat	Get and set additional tool data
Tools	Get and set additional tool data

-- U --

UpdateSeuratObject

Update old Seurat object to accommodate new features

-- V --

VariableFeatures	Highly Variable Features
VariableFeatures.Assay	Highly Variable Features
VariableFeatures.Seurat	Highly Variable Features
VariableFeatures<-	Highly Variable Features
VariableFeatures<-.Assay	Highly Variable Features
VariableFeatures<-.Seurat	Highly Variable Features
Version	Get Version Information
Version.Seurat	Get Version Information

-- W --

WhichCells	Identify cells matching certain criteria
WhichCells.Assay	Identify cells matching certain criteria
WhichCells.Seurat	Identify cells matching certain criteria

-- misc --

$.JackStrawData	'JackStrawData' Methods
$.Seurat	Seurat Methods
$.SeuratCommand	'SeuratCommand' Methods
$<-.Seurat	Seurat Methods
.DollarNames.JackStrawData	'JackStrawData' Methods
.DollarNames.Seurat	Seurat Methods
.DollarNames.SeuratCommand	'SeuratCommand' Methods
[.Assay	'Assay' Methods
[.DimReduc	'DimReduc' Methods
[.Seurat	Seurat Methods
[.SeuratCommand	'SeuratCommand' Methods
[.SpatialImage	'SpatialImage' methods
[[.Assay	'Assay' Methods
[[.DimReduc	'DimReduc' Methods
[[.Seurat	Seurat Methods
[[<--method	'Assay' Methods
[[<--method	Seurat Methods