Man pages for mojaveazure/seurat-object
Data Structures for Single Cell Data

AddMetaData	Add in metadata associated with either cells or features.
AddMetaData-StdAssay	Add in metadata associated with either cells or features.
aggregate	Aggregate Molecules into an Expression Matrix
angles	Radian/Degree Conversions
as.Centroids	Convert Segmentation Layers
as.Graph	Coerce to a 'Graph' Object
as.list.SeuratCommand	Coerce a 'SeuratCommand' to a list
as.matrix.LogMap	Coerce Logical Maps to Matrices
as.Neighbor	Coerce to a 'Neighbor' Object
as.Seurat	Coerce to a 'Seurat' Object
as.sparse	Cast to Sparse
Boundaries	Get, Set, and Query Segmentation Boundaries
cash-.Assay	Layer Data
cash-.Assay5	Layer Data
cash-.Seurat	Cell-Level Meta Data
cash-.SeuratCommand	Command Log Parameter Access
cash-.StdAssay	Layer Data
CastAssay	Cast Assay Layers
CastAssay-StdAssay	Cast Assay Layers
Cells	Cell and Feature Names
CellsByIdentities	Get cell names grouped by identity class
CellsByImage	Get a vector of cell names associated with an image (or set...
Cells-StdAssay	Cell and Feature Names
Centroids-class	The 'Centroids' Class
Centroids-methods	'Centroids' Methods
CheckDots	Check the Use of Dots
CheckFeaturesNames	Check features names format
CheckGC	Conditional Garbage Collection
CheckLayersName	Check layers names for the input list
CheckMatrix	Check Matrix Validity
ClassKey	Generate a Class Key
colMeans-Assay-method	Row and Column Sums and Means
colMeans-Seurat-method	Row and Column Sums and Means
Command	Get SeuratCommands
CreateAssay5Object	Create a v5 Assay object
CreateAssayObject	Create an Assay object
CreateCentroids	Create a 'Centroids' Objects
CreateDimReducObject	Create a DimReduc object
CreateFOV	Create Spatial Coordinates
CreateMolecules	Create a 'Molecules' Object
CreateSegmentation	Create a 'Segmentation' Objects
CreateSeuratObject	Create a 'Seurat' object
Crop	Crop Coordinates
DefaultAssay	Default Assay
DefaultAssay-StdAssay	Default Assay
DefaultDimReduc	Find the default 'DimReduc'
DefaultFOV	Get and Set the Default FOV
DefaultLayer	Default Layer
DefaultLayer-StdAssay	Default Layer
dim.Assay	Feature and Cell Numbers
dim.Assay5	Feature and Cell Numbers
dim.DimReduc	Dimensional Reduction Meta-Information
dimnames.Assay	Assay-Level Feature and Cell Names
dimnames.Assay5	Assay-Level Feature and Cell Names
dimnames.Seurat	Feature and Cell Names
dimnames.StdAssay	Assay-Level Feature and Cell Names
dim.Seurat	Feature and Cell Numbers
dim.StdAssay	Feature and Cell Numbers
Distances	Get the Neighbor nearest neighbors distance matrix
dot-AssayClass	Assay Class Label
dot-BPMatrixMode	'BPCells' Matrix Mode
dot-CalcN	Calculate nCount and nFeature
dot-CheckFmargin	Check Feature Margin
dot-ClassPkg	Get the Package that Defines a Class
dot-Collections	Identify Object Collections
dot-Contains	Get Parent S4 Classes
dot-CreateStdAssay	Generic Assay Creation
dot-DefaultFOV	Find the Default FOV
dot-Deprecate	Deprecate Functions and Arguments
dot-DiskLoad	Disk Loading Function
dot-DollarNames.Assay	Dollar-sign Autocompletion
dot-DollarNames.Assay5	Dollar-sign Autocompletion
dot-DollarNames.Seurat	Dollar-sign Autocompletion
dot-DollarNames.SeuratCommand	Dollar-sign Autocompletion
dot-DollarNames.StdAssay	Dollar-sign Autocompletion
dot-FileMove	Move Files and Directories
dot-FilePath	Find a File Path
dot-FilterObjects	Find Subobjects Of A Certain Class
dot-FindObject	Find A Subobject
dot-GetMethod	Get a Method
dot-IsFutureSeurat	Test Future Compatibility with 'Seurat'
dot-MARGIN	Get the Margin of an Object
dot-PropagateList	Propagate a List
dot-RandomKey	Generate a Random Key
dot-SelectFeatures	Combine and Select Features
dot-SparseSlots	Identify Sparse Slots
dot-Subobjects	Get the Subobject Names
droplevels.LogMap	Drop Unused Logical Map Values
Embeddings	Get Cell Embeddings
EmptyDF	Empty Data Frames
EmptyMatrix	Empty Matrices
ExtractField	Extract delimiter information from a string.
FetchData	Access cellular data
FOV-methods	'FOV' Methods
FOV-validity	FOV Validity
GetImage	Get image data
GetTissueCoordinates	Get tissue coordinates
Graph-class	The Graph Class
Idents	Get, set, and manipulate an object's identity classes
Images	Pull spatial image names
Indices	Get Neighbor nearest neighbor index matrices
intersect.LogMap	Find Common Logical Map Values
IsGlobal	Is an object global/persistent?
IsMatrixEmpty	Check if a matrix is empty
IsNamedList	Check List Names
IsSparse	Is a Matrix Sparse
JackStrawData-class	The JackStrawData Class
JackStrawData-methods	'JackStrawData' Methods
JS	Get and set JackStraw information
Key	Get and set object keys
labels.LogMap	Find Observations by Value
Loadings	Get and set feature loadings
LogMap-class	A Logical Map
LogMap-validity	Logical Map Validity
LogSeuratCommand	Log a command
MatchCells	Match Cells
merge.Assay	Merge Assays
merge.Assay5	Merge Assays
merge.DimReduc	Merge Dimensional Reductions
merge.Seurat	Merge Seurat Objects
merge.StdAssay	Merge Assays
Misc	Get and set miscellaneous data
Misc-StdAssay	Get and set miscellaneous data
Molecules-class	The Spatial Molecules Class
Molecules-methods	'Molecules' Methods
names.Seurat	Subobject Names
Neighbor-class	The Neighbor class
Neighbor-methods	'Neighbor' Methods
NNIndex	Get Neighbor algorithm index
ObjectAccess	Query Specific Object Types
old-assign	Original double-bracket assign
oldseurat-class	The Seurat Class
Overlay	Overlay 'Spatial' Objects Over One Another
pbmc_small	A small example version of the PBMC dataset
PolyVtx	Polygon Vertices
print.DimReduc	Print Top Feature Loadings
Project	Get and set project information
Radius	Get the spot radius from an image
RandomName	Generate a random name
reexports	Objects exported from other packages
RegisterSparseMatrix	Register Sparse Matrix Classes
RenameAssays	Rename assays in a 'Seurat' object
RenameCells	Rename cells
RenameCells-StdAssay	Rename cells
RowMergeSparseMatrices	Merge Sparse Matrices by Row
s4list	S4/List Conversion
Segmentation-class	The 'Segmentation' Class
Segmentation-methods	'Segmentation' Methods
set-if-na	Set If or If Not 'NA'
set-if-null	Set If or If Not 'NULL'
Seurat-class	The Seurat Class
SeuratCommand-class	The 'SeuratCommand' Class
SeuratObject-package	SeuratObject: Data Structures for Single Cell Data
Seurat-validity	Seurat Object Validity
show-Assay-method	V3 Assay Overview
show-DimReduc-method	Dimensional Reduction Overview
show-Graph-method	Graph Object Overview
show-LogMap-method	'LogMap' Object Overview
show-oldseurat-method	Old Seurat Object Overview
show-SeuratCommand-method	Command Log Overview
show-Seurat-method	Seurat Object Overview
show-StdAssay-method	V5 Assay Overview
Simplify	Simplify Geometry
SparseEmptyMatrix	Generate empty dgC sparse matrix
SpatialImage-methods	'SpatialImage' methods
split.Assay	Split an Assay
split.Assay5	Split an Assay
SplitLayers	Split and Join Layers Together
split.Seurat	Split an Assay
split.StdAssay	Split an Assay
Stdev	Get the standard deviations for an object
StitchMatrix	Stitch Matrices Together
sub-.Assay	Layer Data
sub-.Assay5	Layer Data
sub-.DimReduc	Get Feature Loadings
sub-LogMap-method	Matrix-like Subsetting for Logical Maps
subset.Assay	Subset an Assay
subset.Assay5	Subset an Assay
subset.DimReduc	Subset a Dimensional Reduction
subset.Seurat	Subset 'Seurat' Objects
subset.StdAssay	Subset an Assay
sub-.SeuratCommand	Command Log Data Access
sub-.StdAssay	Layer Data
sub-sub-.Assay	Feature-Level Meta Data
sub-sub-.Assay5	Feature-Level Meta Data
sub-sub-.DimReduc	Get Cell Embeddings
sub-sub-LogMap-internal-method	'LogMap' Interaction Methods
sub-subset-Seurat	Add Subobjects
sub-subset-Seurat-character-missing-StdAssay-method	Add Subobjects
sub-subset-Seurat-NULL	Remove Subobjects and Cell-Level Meta Data
sub-sub-.Seurat	Subobjects and Cell-Level Meta Data
sub-sub-.StdAssay	Feature-Level Meta Data
Theta	Get the offset angle
Tool	Get and Set Additional Tool Data
UpdateSeuratObject	Update old Seurat object to accommodate new features
UpdateSlots	Update slots in an object
v5-assay-summaries	V5 Assay Summaries
Version	Get Version Information
WhichCells	Identify cells matching certain criteria