Man pages for SeuratObject
Data Structures for Single Cell Data

AddMetaDataAdd in metadata associated with either cells or features.
AddMetaData-StdAssayAdd in metadata associated with either cells or features.
aggregateAggregate Molecules into an Expression Matrix
anglesRadian/Degree Conversions
as.CentroidsConvert Segmentation Layers
as.GraphCoerce to a 'Graph' Object
as.list.SeuratCommandCoerce a 'SeuratCommand' to a list
as.matrix.LogMapCoerce Logical Maps to Matrices
as.NeighborCoerce to a 'Neighbor' Object
as.SeuratCoerce to a 'Seurat' Object
as.sparseCast to Sparse
BoundariesGet, Set, and Query Segmentation Boundaries
cash-.AssayLayer Data
cash-.Assay5Layer Data
cash-.SeuratCell-Level Meta Data
cash-.SeuratCommandCommand Log Parameter Access
cash-.StdAssayLayer Data
CastAssayCast Assay Layers
CastAssay-StdAssayCast Assay Layers
CellsCell and Feature Names
CellsByIdentitiesGet cell names grouped by identity class
CellsByImageGet a vector of cell names associated with an image (or set...
Cells-StdAssayCell and Feature Names
Centroids-classThe 'Centroids' Class
Centroids-methods'Centroids' Methods
CheckDotsCheck the Use of Dots
CheckFeaturesNamesCheck features names format
CheckGCConditional Garbage Collection
CheckLayersNameCheck layers names for the input list
CheckMatrixCheck Matrix Validity
ClassKeyGenerate a Class Key
colMeans-Assay-methodRow and Column Sums and Means
colMeans-Seurat-methodRow and Column Sums and Means
CommandGet SeuratCommands
CreateAssay5ObjectCreate a v5 Assay object
CreateAssayObjectCreate an Assay object
CreateCentroidsCreate a 'Centroids' Objects
CreateDimReducObjectCreate a DimReduc object
CreateFOVCreate Spatial Coordinates
CreateMoleculesCreate a 'Molecules' Object
CreateSegmentationCreate a 'Segmentation' Objects
CreateSeuratObjectCreate a 'Seurat' object
CropCrop Coordinates
DefaultAssayDefault Assay
DefaultAssay-StdAssayDefault Assay
DefaultDimReducFind the default 'DimReduc'
DefaultFOVGet and Set the Default FOV
DefaultLayerDefault Layer
DefaultLayer-StdAssayDefault Layer
dim.AssayFeature and Cell Numbers
dim.Assay5Feature and Cell Numbers
dim.DimReducDimensional Reduction Meta-Information
dimnames.AssayAssay-Level Feature and Cell Names
dimnames.Assay5Assay-Level Feature and Cell Names
dimnames.SeuratFeature and Cell Names
dimnames.StdAssayAssay-Level Feature and Cell Names
dim.SeuratFeature and Cell Numbers
dim.StdAssayFeature and Cell Numbers
DistancesGet the Neighbor nearest neighbors distance matrix
dot-AssayClassAssay Class Label
dot-BPMatrixMode'BPCells' Matrix Mode
dot-CalcNCalculate nCount and nFeature
dot-CheckFmarginCheck Feature Margin
dot-ClassPkgGet the Package that Defines a Class
dot-CollectionsIdentify Object Collections
dot-ContainsGet Parent S4 Classes
dot-CreateStdAssayGeneric Assay Creation
dot-DefaultFOVFind the Default FOV
dot-DeprecateDeprecate Functions and Arguments
dot-DiskLoadDisk Loading Function
dot-DollarNames.AssayDollar-sign Autocompletion
dot-DollarNames.Assay5Dollar-sign Autocompletion
dot-DollarNames.SeuratDollar-sign Autocompletion
dot-DollarNames.SeuratCommandDollar-sign Autocompletion
dot-DollarNames.StdAssayDollar-sign Autocompletion
dot-FileMoveMove Files and Directories
dot-FilePathFind a File Path
dot-FilterObjectsFind Subobjects Of A Certain Class
dot-FindObjectFind A Subobject
dot-GetMethodGet a Method
dot-IsFutureSeuratTest Future Compatibility with 'Seurat'
dot-MARGINGet the Margin of an Object
dot-PropagateListPropagate a List
dot-RandomKeyGenerate a Random Key
dot-SelectFeaturesCombine and Select Features
dot-SparseSlotsIdentify Sparse Slots
dot-SubobjectsGet the Subobject Names
droplevels.LogMapDrop Unused Logical Map Values
EmbeddingsGet Cell Embeddings
EmptyDFEmpty Data Frames
EmptyMatrixEmpty Matrices
ExtractFieldExtract delimiter information from a string.
FetchDataAccess cellular data
FOV-methods'FOV' Methods
FOV-validityFOV Validity
GetImageGet image data
GetTissueCoordinatesGet tissue coordinates
Graph-classThe Graph Class
IdentsGet, set, and manipulate an object's identity classes
ImagesPull spatial image names
IndicesGet Neighbor nearest neighbor index matrices
intersect.LogMapFind Common Logical Map Values
IsGlobalIs an object global/persistent?
IsMatrixEmptyCheck if a matrix is empty
IsNamedListCheck List Names
IsSparseIs a Matrix Sparse
JackStrawData-classThe JackStrawData Class
JackStrawData-methods'JackStrawData' Methods
JSGet and set JackStraw information
KeyGet and set object keys
labels.LogMapFind Observations by Value
LoadingsGet and set feature loadings
LogMap-classA Logical Map
LogMap-validityLogical Map Validity
LogSeuratCommandLog a command
MatchCellsMatch Cells
merge.AssayMerge Assays
merge.Assay5Merge Assays
merge.DimReducMerge Dimensional Reductions
merge.SeuratMerge Seurat Objects
merge.StdAssayMerge Assays
MiscGet and set miscellaneous data
Misc-StdAssayGet and set miscellaneous data
Molecules-classThe Spatial Molecules Class
Molecules-methods'Molecules' Methods
names.SeuratSubobject Names
Neighbor-classThe Neighbor class
Neighbor-methods'Neighbor' Methods
NNIndexGet Neighbor algorithm index
ObjectAccessQuery Specific Object Types
old-assignOriginal double-bracket assign
oldseurat-classThe Seurat Class
OverlayOverlay 'Spatial' Objects Over One Another
pbmc_smallA small example version of the PBMC dataset
PolyVtxPolygon Vertices
print.DimReducPrint Top Feature Loadings
ProjectGet and set project information
RadiusGet the spot radius from an image
RandomNameGenerate a random name
reexportsObjects exported from other packages
RegisterSparseMatrixRegister Sparse Matrix Classes
RenameAssaysRename assays in a 'Seurat' object
RenameCellsRename cells
RenameCells-StdAssayRename cells
RowMergeSparseMatricesMerge Sparse Matrices by Row
s4listS4/List Conversion
Segmentation-classThe 'Segmentation' Class
Segmentation-methods'Segmentation' Methods
set-if-naSet If or If Not 'NA'
set-if-nullSet If or If Not 'NULL'
Seurat-classThe Seurat Class
SeuratCommand-classThe 'SeuratCommand' Class
SeuratObject-packageSeuratObject: Data Structures for Single Cell Data
Seurat-validitySeurat Object Validity
show-Assay-methodV3 Assay Overview
show-DimReduc-methodDimensional Reduction Overview
show-Graph-methodGraph Object Overview
show-LogMap-method'LogMap' Object Overview
show-oldseurat-methodOld Seurat Object Overview
show-SeuratCommand-methodCommand Log Overview
show-Seurat-methodSeurat Object Overview
show-StdAssay-methodV5 Assay Overview
SimplifySimplify Geometry
SparseEmptyMatrixGenerate empty dgC sparse matrix
SpatialImage-methods'SpatialImage' methods
split.AssaySplit an Assay
split.Assay5Split an Assay
SplitLayersSplit and Join Layers Together
split.SeuratSplit an Assay
split.StdAssaySplit an Assay
StdevGet the standard deviations for an object
StitchMatrixStitch Matrices Together
sub-.AssayLayer Data
sub-.Assay5Layer Data
sub-.DimReducGet Feature Loadings
sub-LogMap-methodMatrix-like Subsetting for Logical Maps
subset.AssaySubset an Assay
subset.Assay5Subset an Assay
subset.DimReducSubset a Dimensional Reduction
subset.SeuratSubset 'Seurat' Objects
subset.StdAssaySubset an Assay
sub-.SeuratCommandCommand Log Data Access
sub-.StdAssayLayer Data
sub-sub-.AssayFeature-Level Meta Data
sub-sub-.Assay5Feature-Level Meta Data
sub-sub-.DimReducGet Cell Embeddings
sub-sub-LogMap-internal-method'LogMap' Interaction Methods
sub-subset-SeuratAdd Subobjects
sub-subset-Seurat-character-missing-StdAssay-methodAdd Subobjects
sub-subset-Seurat-NULLRemove Subobjects and Cell-Level Meta Data
sub-sub-.SeuratSubobjects and Cell-Level Meta Data
sub-sub-.StdAssayFeature-Level Meta Data
ThetaGet the offset angle
ToolGet and Set Additional Tool Data
UpdateSeuratObjectUpdate old Seurat object to accommodate new features
UpdateSlotsUpdate slots in an object
v5-assay-summariesV5 Assay Summaries
VersionGet Version Information
WhichCellsIdentify cells matching certain criteria
SeuratObject documentation built on May 29, 2024, 12:31 p.m.