SeuratObject-package	SeuratObject-package
$.FOV	FOV-methods
$.JackStrawData	JackStrawData-methods
$.Seurat	Seurat-methods
$.SeuratCommand	SeuratCommand-methods
$<-.Seurat	Seurat-methods
%!NA%	set-if-na
%!na%	set-if-na
%iff%	set-if-null
%NA%	set-if-na
%na%	set-if-na
%||%	set-if-null
.Contains	dot-Contains
.DefaultFOV	dot-DefaultFOV
.DollarNames.JackStrawData	JackStrawData-methods
.DollarNames.Seurat	Seurat-methods
.DollarNames.SeuratCommand	SeuratCommand-methods
AddMetaData	AddMetaData
AddMetaData.Assay	AddMetaData
AddMetaData.Seurat	AddMetaData
AddSamples	Seurat-methods
aggregate	aggregate
aggregate.FOV	aggregate
aggregate.Molecules	aggregate
Angles	Angles
as.Centroids	as.Centroids
as.Centroids.Segmentation	as.Centroids
as.Graph	as.Graph
as.Graph.Matrix	as.Graph
as.Graph.matrix	as.Graph
as.Graph.Neighbor	as.Graph
as.list.SeuratCommand	SeuratCommand-methods
as.logical.JackStrawData	JackStrawData-methods
as.Neighbor	as.Neighbor
as.Neighbor.Graph	as.Neighbor
as.Segmentation	as.Centroids
as.Segmentation.Centroids	as.Centroids
as.Seurat	as.Seurat
as.sparse	as.sparse
as.sparse.data.frame	as.sparse
as.sparse.Matrix	as.sparse
as.sparse.matrix	as.sparse
as.sparse.ngCMatrix	as.sparse
Assay	Assay-class
Assay-class	Assay-class
Assay-methods	Assay-methods
AssayData	AssayData
Assays	ObjectAccess
AttachDeps	AttachDeps
Boundaries	Boundaries
Boundaries.FOV	Boundaries
Cells	Cells
Cells.Centroids	Centroids-methods
Cells.default	Cells
Cells.DimReduc	Cells
Cells.FOV	FOV-methods
Cells.Neighbor	Cells
Cells.Segmentation	Segmentation-methods
Cells.SpatialImage	SpatialImage-methods
CellsByIdentities	CellsByIdentities
CellsByImage	CellsByImage
Centroids-class	Centroids-class
Centroids-methods	Centroids-methods
CheckDots	CheckDots
CheckGC	CheckGC
CheckMatrix	CheckMatrix
CheckMatrix.default	CheckMatrix
CheckMatrix.dMatrix	CheckMatrix
CheckMatrix.lMatrix	CheckMatrix
colMeans	reexports
colMeans,Assay-method	Assay-methods
colMeans,Seurat-method	Seurat-methods
colSums	reexports
colSums,Assay-method	Assay-methods
colSums,Seurat-method	Seurat-methods
Command	Command
Command.Seurat	Command
coordinates,Segmentation-method	Segmentation-methods
CreateAssayObject	CreateAssayObject
CreateCentroids	CreateCentroids
CreateDimReducObject	CreateDimReducObject
CreateFOV	CreateFOV
CreateFOV.Centroids	CreateFOV
CreateFOV.data.frame	CreateFOV
CreateFOV.list	CreateFOV
CreateFOV.Segmentation	CreateFOV
CreateMolecules	CreateMolecules
CreateMolecules.data.frame	CreateMolecules
CreateMolecules.Molecules	CreateMolecules
CreateMolecules.NULL	CreateMolecules
CreateSegmentation	CreateSegmentation
CreateSegmentation.data.frame	CreateSegmentation
CreateSegmentation.Segmentation	CreateSegmentation
CreateSeuratObject	CreateSeuratObject
CreateSeuratObject.Assay	CreateSeuratObject
CreateSeuratObject.default	CreateSeuratObject
Crop	Crop
Crop.FOV	Crop
DefaultAssay	DefaultAssay
DefaultAssay.Assay	DefaultAssay
DefaultAssay.DimReduc	DefaultAssay
DefaultAssay.Graph	DefaultAssay
DefaultAssay.Seurat	DefaultAssay
DefaultAssay.SeuratCommand	DefaultAssay
DefaultAssay.SpatialImage	SpatialImage-methods
DefaultAssay<-	DefaultAssay
DefaultAssay<-.Assay	DefaultAssay
DefaultAssay<-.DimReduc	DefaultAssay
DefaultAssay<-.Graph	DefaultAssay
DefaultAssay<-.Seurat	DefaultAssay
DefaultAssay<-.SpatialImage	SpatialImage-methods
DefaultBoundary	Boundaries
DefaultBoundary.FOV	Boundaries
DefaultBoundary<-	Boundaries
DefaultBoundary<-.FOV	Boundaries
DefaultDimReduc	DefaultDimReduc
DefaultFOV	DefaultFOV
DefaultFOV.Seurat	DefaultFOV
DefaultFOV<-	DefaultFOV
DefaultFOV<-.Seurat	DefaultFOV
Degrees	Angles
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	DimReduc-class
DimReduc-class	DimReduc-class
DimReduc-methods	DimReduc-methods
Distances	Distances
Distances.Neighbor	Distances
droplevels.Seurat	Idents
Embeddings	Embeddings
Embeddings.DimReduc	Embeddings
Embeddings.Seurat	Embeddings
EmptyDF	EmptyDF
Features	Cells
Features.FOV	FOV-methods
Features.Molecules	Molecules-methods
FetchData	FetchData
FetchData.DimReduc	FetchData
FetchData.FOV	FOV-methods
FetchData.Seurat	FetchData
FilterObjects	FilterObjects
FOV	FOV-class
FOV-class	FOV-class
FOV-methods	FOV-methods
GetAssayData	AssayData
GetAssayData.Assay	AssayData
GetAssayData.Seurat	AssayData
GetImage	GetImage
GetImage.Seurat	GetImage
GetImage.SpatialImage	SpatialImage-methods
GetTissueCoordinates	GetTissueCoordinates
GetTissueCoordinates.Centroids	Centroids-methods
GetTissueCoordinates.FOV	FOV-methods
GetTissueCoordinates.Molecules	Molecules-methods
GetTissueCoordinates.Segmentation	Segmentation-methods
GetTissueCoordinates.Seurat	GetTissueCoordinates
GetTissueCoordinates.SpatialImage	SpatialImage-methods
Graph	Graph-class
Graph-class	Graph-class
Graphs	ObjectAccess
handlers	reexports
head.Assay	Assay-methods
head.Seurat	Seurat-methods
HVFInfo	VariableFeatures
HVFInfo.Assay	VariableFeatures
HVFInfo.Seurat	VariableFeatures
Idents	Idents
Idents.Seurat	Idents
Idents<-	Idents
Idents<-.Seurat	Idents
Images	Images
Index	Index
Index.Neighbor	Index
Index<-	Index
Index<-.Neighbor	Index
Indices	Indices
Indices.Neighbor	Indices
is.finite.Centroids	Centroids-methods
is.infinite.Centroids	Centroids-methods
IsGlobal	IsGlobal
IsGlobal.default	IsGlobal
IsGlobal.DimReduc	IsGlobal
IsGlobal.SpatialImage	SpatialImage-methods
IsMatrixEmpty	IsMatrixEmpty
IsNamedList	IsNamedList
IsS4List	s4list
JackStrawData	JackStrawData-class
JackStrawData-class	JackStrawData-class
JackStrawData-methods	JackStrawData-methods
JS	JS
JS.DimReduc	JS
JS.JackStrawData	JS
JS<-	JS
JS<-.DimReduc	JS
JS<-.JackStrawData	JS
Key	Key
Key.Assay	Key
Key.character	KeyMixin-class
Key.DimReduc	Key
Key.KeyMixin	KeyMixin-class
Key.Seurat	Key
Key.SpatialImage	SpatialImage-methods
Key<-	Key
Key<-.Assay	Key
Key<-.DimReduc	Key
Key<-.KeyMixin	KeyMixin-class
Key<-.SpatialImage	SpatialImage-methods
KeyMixin	KeyMixin-class
KeyMixin-class	KeyMixin-class
Keys	Key
Keys.FOV	FOV-methods
Keys.Seurat	Key
length.Centroids	Centroids-methods
length.DimReduc	DimReduc-methods
length.FOV	FOV-methods
lengths.Centroids	Centroids-methods
lengths.Segmentation	Segmentation-methods
levels.Seurat	Idents
levels<-.Seurat	Idents
ListToS4	s4list
Loadings	Loadings
Loadings.DimReduc	Loadings
Loadings.Seurat	Loadings
Loadings<-	Loadings
Loadings<-.DimReduc	Loadings
LogMap	LogMap-class
LogMap-class	LogMap-class
LogSeuratCommand	LogSeuratCommand
MatchCells	MatchCells
MatchCells.character	MatchCells
MatchCells.NULL	MatchCells
MatchCells.numeric	MatchCells
merge	Seurat-methods
merge.Assay	Assay-methods
merge.DimReduc	DimReduc-methods
merge.Seurat	Seurat-methods
MergeSeurat	Seurat-methods
Misc	Misc
Misc.Assay	Misc
Misc.DimReduc	Misc
Misc.Seurat	Misc
Misc<-	Misc
Misc<-.Assay	Misc
Misc<-.DimReduc	Misc
Misc<-.Seurat	Misc
Molecules	Boundaries
Molecules-class	Molecules-class
Molecules-methods	Molecules-methods
Molecules.FOV	Boundaries
names.DimReduc	DimReduc-methods
names.FOV	FOV-methods
names.Seurat	Seurat-methods
Neighbor	Neighbor-class
Neighbor-class	Neighbor-class
Neighbor-methods	Neighbor-methods
Neighbors	ObjectAccess
Overlay	Overlay
Overlay,Centroids,SpatialPolygons-method	Overlay
Overlay,FOV,FOV-method	Overlay
Overlay,FOV,Spatial-method	Overlay
Overlay,FOV,SpatialPolygons-method	Overlay
Overlay,Molecules,SpatialPolygons-method	Overlay
Overlay,Segmentation,SpatialPolygons-method	Overlay
PackageCheck	PackageCheck
pbmc_small	pbmc_small
plan	reexports
PolyVtx	PolyVtx
print	DimReduc-methods
print.DimReduc	DimReduc-methods
Project	Project
Project.Seurat	Project
Project<-	Project
Project<-.Seurat	Project
Radians	Angles
Radius	Radius
Radius.Centroids	Centroids-methods
Radius.SpatialImage	SpatialImage-methods
RandomName	RandomName
Reductions	ObjectAccess
reexports	reexports
RenameAssays	RenameAssays
RenameCells	RenameCells
RenameCells.Assay	RenameCells
RenameCells.Centroids	Centroids-methods
RenameCells.DimReduc	RenameCells
RenameCells.FOV	FOV-methods
RenameCells.Neighbor	RenameCells
RenameCells.Segmentation	Segmentation-methods
RenameCells.Seurat	RenameCells
RenameCells.SpatialImage	SpatialImage-methods
RenameIdent	Idents
RenameIdents	Idents
RenameIdents.Seurat	Idents
ReorderIdent	Idents
ReorderIdent.Seurat	Idents
rowMeans	reexports
rowMeans,Assay-method	Assay-methods
rowMeans,Seurat-method	Seurat-methods
RowMergeSparseMatrices	RowMergeSparseMatrices
rowSums	reexports
rowSums,Assay-method	Assay-methods
rowSums,Seurat-method	Seurat-methods
s4list	s4list
S4ToList	s4list
S4ToList.default	s4list
S4ToList.list	s4list
Segmentation-class	Segmentation-class
Segmentation-methods	Segmentation-methods
set-if-na	set-if-na
set-if-null	set-if-null
SetAssayData	AssayData
SetAssayData.Assay	AssayData
SetAssayData.Seurat	AssayData
SetDimReduction	CreateDimReducObject
SetIdent	Idents
SetIdent.Seurat	Idents
Seurat	Seurat-class
seurat	oldseurat-class
Seurat-class	Seurat-class
seurat-class	oldseurat-class
Seurat-methods	Seurat-methods
SeuratAccess	AddMetaData
SeuratCommand	SeuratCommand-class
SeuratCommand-class	SeuratCommand-class
SeuratCommand-methods	SeuratCommand-methods
SeuratObject	SeuratObject-package
show,Assay-method	Assay-methods
show,Centroids-method	Centroids-methods
show,DimReduc-method	DimReduc-methods
show,FOV-method	FOV-methods
show,JackStrawData-method	JackStrawData-methods
show,LogMap-method	LogMap-class
show,Molecules-method	Molecules-methods
show,Neighbor-method	Neighbor-methods
show,Segmentation-method	Segmentation-methods
show,Seurat-method	Seurat-methods
show,seurat-method	oldseurat-class
show,SeuratCommand-method	SeuratCommand-methods
show,SpatialImage-method	SpatialImage-methods
Simplify	Simplify
Simplify.Spatial	Simplify
SpatialImage	SpatialImage-class
SpatialImage-class	SpatialImage-class
SpatialImage-methods	SpatialImage-methods
SpatiallyVariableFeatures	VariableFeatures
SpatiallyVariableFeatures.Assay	VariableFeatures
SpatiallyVariableFeatures.Seurat	VariableFeatures
StashIdent	Idents
StashIdent.Seurat	Idents
Stdev	Stdev
Stdev.DimReduc	Stdev
Stdev.Seurat	Stdev
subset	Seurat-methods
subset.Assay	Assay-methods
subset.Centroids	Centroids-methods
subset.DimReduc	DimReduc-methods
subset.FOV	FOV-methods
subset.Molecules	Molecules-methods
subset.Segmentation	Segmentation-methods
subset.Seurat	Seurat-methods
subset.SpatialImage	SpatialImage-methods
SVFInfo	VariableFeatures
SVFInfo.Assay	VariableFeatures
SVFInfo.Seurat	VariableFeatures
tail.Assay	Assay-methods
tail.Seurat	Seurat-methods
Theta	Theta
Theta.Centroids	Centroids-methods
Tool	Tool
Tool.Seurat	Tool
Tool<-	Tool
Tool<-.Seurat	Tool
Tools	Tool
UpdateSeuratObject	UpdateSeuratObject
UpdateSlots	UpdateSlots
VariableFeatures	VariableFeatures
VariableFeatures.Assay	VariableFeatures
VariableFeatures.Seurat	VariableFeatures
VariableFeatures<-	VariableFeatures
VariableFeatures<-.Assay	VariableFeatures
VariableFeatures<-.Seurat	VariableFeatures
Version	Version
Version.Seurat	Version
WhichCells	WhichCells
WhichCells.Assay	WhichCells
WhichCells.Seurat	WhichCells
with_progress	reexports
[,Centroids,character,ANY,ANY-method	Centroids-methods
[,Centroids,numeric,ANY,ANY-method	Centroids-methods
[,Segmentation,ANY,ANY,ANY-method	Segmentation-methods
[.Assay	Assay-methods
[.DimReduc	DimReduc-methods
[.FOV	FOV-methods
[.Seurat	Seurat-methods
[.SeuratCommand	SeuratCommand-methods
[.SpatialImage	SpatialImage-methods
[[,LogMap,character,missing-method	LogMap-class
[[,LogMap,missing,missing-method	LogMap-class
[[,LogMap,NULL,missing-method	LogMap-class
[[.Assay	Assay-methods
[[.DimReduc	DimReduc-methods
[[.FOV	FOV-methods
[[.Seurat	Seurat-methods
[[<-,Assay,ANY,ANY,ANY-method	Assay-methods
[[<-,FOV,character,missing,Centroids-method	FOV-methods
[[<-,FOV,character,missing,Molecules-method	FOV-methods
[[<-,FOV,character,missing,NULL-method	FOV-methods
[[<-,FOV,character,missing,Segmentation-method	FOV-methods
[[<-,LogMap,character,missing,character-method	LogMap-class
[[<-,LogMap,character,missing,integer-method	LogMap-class
[[<-,LogMap,character,missing,NULL-method	LogMap-class
[[<-,LogMap,character,missing,numeric-method	LogMap-class
[[<-,Seurat,ANY,ANY,ANY-method	Seurat-methods
