# Generated by roxygen2: do not edit by hand

S3method("$",Assay)
S3method("$",Assay5)
S3method("$",FOV)
S3method("$",JackStrawData)
S3method("$",Seurat)
S3method("$",SeuratCommand)
S3method("$",StdAssay)
S3method("$<-",Assay)
S3method("$<-",Assay5)
S3method("$<-",Seurat)
S3method("$<-",StdAssay)
S3method("DefaultAssay<-",Assay)
S3method("DefaultAssay<-",Assay5)
S3method("DefaultAssay<-",DimReduc)
S3method("DefaultAssay<-",Graph)
S3method("DefaultAssay<-",Seurat)
S3method("DefaultAssay<-",SpatialImage)
S3method("DefaultAssay<-",StdAssay)
S3method("DefaultBoundary<-",FOV)
S3method("DefaultDimReduc<-",Seurat)
S3method("DefaultFOV<-",Seurat)
S3method("DefaultLayer<-",Assay5)
S3method("DefaultLayer<-",StdAssay)
S3method("Idents<-",Seurat)
S3method("Index<-",Neighbor)
S3method("JS<-",DimReduc)
S3method("JS<-",JackStrawData)
S3method("Key<-",Assay)
S3method("Key<-",Assay5)
S3method("Key<-",DimReduc)
S3method("Key<-",KeyMixin)
S3method("Key<-",SpatialImage)
S3method("LayerData<-",Assay)
S3method("LayerData<-",Assay5)
S3method("LayerData<-",Seurat)
S3method("LayerData<-",StdAssay)
S3method("Loadings<-",DimReduc)
S3method("Misc<-",Assay)
S3method("Misc<-",Assay5)
S3method("Misc<-",DimReduc)
S3method("Misc<-",Seurat)
S3method("Misc<-",StdAssay)
S3method("Project<-",Seurat)
S3method("Tool<-",Seurat)
S3method("VariableFeatures<-",Assay)
S3method("VariableFeatures<-",Assay5)
S3method("VariableFeatures<-",Seurat)
S3method("VariableFeatures<-",StdAssay)
S3method("[",Assay)
S3method("[",Assay5)
S3method("[",DimReduc)
S3method("[",FOV)
S3method("[",Seurat)
S3method("[",SeuratCommand)
S3method("[",SpatialImage)
S3method("[",StdAssay)
S3method("[[",Assay)
S3method("[[",Assay5)
S3method("[[",DimReduc)
S3method("[[",FOV)
S3method("[[",Seurat)
S3method("[[",StdAssay)
S3method("dimnames<-",Assay)
S3method("dimnames<-",Assay5)
S3method("dimnames<-",Seurat)
S3method("dimnames<-",StdAssay)
S3method("levels<-",Seurat)
S3method(.AssayClass,Assay5T)
S3method(.AssayClass,StdAssay)
S3method(.AssayClass,default)
S3method(.CalcN,Assay)
S3method(.CalcN,StdAssay)
S3method(.CalcN,default)
S3method(.ClassPkg,DelayedArray)
S3method(.ClassPkg,R6)
S3method(.ClassPkg,R6ClassGenerator)
S3method(.ClassPkg,default)
S3method(.CreateStdAssay,Matrix)
S3method(.CreateStdAssay,default)
S3method(.CreateStdAssay,list)
S3method(.CreateStdAssay,matrix)
S3method(.DiskLoad,"10xMatrixH5")
S3method(.DiskLoad,AnnDataMatrixH5)
S3method(.DiskLoad,DelayedMatrix)
S3method(.DiskLoad,H5ADMatrix)
S3method(.DiskLoad,HDF5Matrix)
S3method(.DiskLoad,IterableMatrix)
S3method(.DiskLoad,MatrixDir)
S3method(.DiskLoad,MatrixH5)
S3method(.DiskLoad,TileDBMatrix)
S3method(.DiskLoad,default)
S3method(.DollarNames,Assay)
S3method(.DollarNames,Assay5)
S3method(.DollarNames,FOV)
S3method(.DollarNames,JackStrawData)
S3method(.DollarNames,Seurat)
S3method(.DollarNames,SeuratCommand)
S3method(.DollarNames,StdAssay)
S3method(.FilePath,DelayedMatrix)
S3method(.FilePath,IterableMatrix)
S3method(.FilePath,default)
S3method(.MARGIN,Assay5T)
S3method(.MARGIN,CsparseMatrix)
S3method(.MARGIN,RsparseMatrix)
S3method(.MARGIN,default)
S3method(.MARGIN,spam)
S3method(.SparseSlots,CsparseMatrix)
S3method(.SparseSlots,RsparseMatrix)
S3method(.SparseSlots,spam)
S3method(AddMetaData,Assay)
S3method(AddMetaData,Assay5)
S3method(AddMetaData,Seurat)
S3method(AddMetaData,StdAssay)
S3method(Assays,Seurat)
S3method(Boundaries,FOV)
S3method(CastAssay,Assay5)
S3method(CastAssay,Seurat)
S3method(CastAssay,StdAssay)
S3method(Cells,Assay5)
S3method(Cells,Centroids)
S3method(Cells,DimReduc)
S3method(Cells,FOV)
S3method(Cells,Graph)
S3method(Cells,Neighbor)
S3method(Cells,Segmentation)
S3method(Cells,Seurat)
S3method(Cells,SpatialImage)
S3method(Cells,StdAssay)
S3method(Cells,default)
S3method(CheckMatrix,dMatrix)
S3method(CheckMatrix,default)
S3method(CheckMatrix,lMatrix)
S3method(Command,Seurat)
S3method(CreateCentroids,Centroids)
S3method(CreateCentroids,default)
S3method(CreateFOV,Centroids)
S3method(CreateFOV,Segmentation)
S3method(CreateFOV,data.frame)
S3method(CreateFOV,list)
S3method(CreateMolecules,"NULL")
S3method(CreateMolecules,Molecules)
S3method(CreateMolecules,data.frame)
S3method(CreateSegmentation,Segmentation)
S3method(CreateSegmentation,data.frame)
S3method(CreateSegmentation,sf)
S3method(CreateSeuratObject,Assay)
S3method(CreateSeuratObject,Assay5)
S3method(CreateSeuratObject,StdAssay)
S3method(CreateSeuratObject,default)
S3method(Crop,Centroids)
S3method(Crop,FOV)
S3method(Crop,Molecules)
S3method(Crop,Segmentation)
S3method(DefaultAssay,Assay)
S3method(DefaultAssay,Assay5)
S3method(DefaultAssay,DimReduc)
S3method(DefaultAssay,Graph)
S3method(DefaultAssay,Seurat)
S3method(DefaultAssay,SeuratCommand)
S3method(DefaultAssay,SpatialImage)
S3method(DefaultAssay,StdAssay)
S3method(DefaultBoundary,FOV)
S3method(DefaultFOV,Seurat)
S3method(DefaultLayer,Assay)
S3method(DefaultLayer,Assay5)
S3method(DefaultLayer,StdAssay)
S3method(Distances,Neighbor)
S3method(Embeddings,DimReduc)
S3method(Embeddings,Seurat)
S3method(Features,Assay)
S3method(Features,Assay5)
S3method(Features,DimReduc)
S3method(Features,FOV)
S3method(Features,Molecules)
S3method(Features,Seurat)
S3method(Features,StdAssay)
S3method(FetchData,Assay)
S3method(FetchData,Assay5)
S3method(FetchData,DimReduc)
S3method(FetchData,FOV)
S3method(FetchData,Molecules)
S3method(FetchData,Seurat)
S3method(FetchData,StdAssay)
S3method(GetAssayData,Assay)
S3method(GetAssayData,Seurat)
S3method(GetAssayData,StdAssay)
S3method(GetImage,Seurat)
S3method(GetImage,SpatialImage)
S3method(GetTissueCoordinates,Centroids)
S3method(GetTissueCoordinates,FOV)
S3method(GetTissueCoordinates,Molecules)
S3method(GetTissueCoordinates,Segmentation)
S3method(GetTissueCoordinates,Seurat)
S3method(GetTissueCoordinates,SpatialImage)
S3method(HVFInfo,Assay)
S3method(HVFInfo,Assay5)
S3method(HVFInfo,Seurat)
S3method(HVFInfo,StdAssay)
S3method(Idents,Seurat)
S3method(Index,Neighbor)
S3method(Indices,Neighbor)
S3method(IsGlobal,DimReduc)
S3method(IsGlobal,SpatialImage)
S3method(IsGlobal,default)
S3method(IsMatrixEmpty,default)
S3method(JS,DimReduc)
S3method(JS,JackStrawData)
S3method(JoinLayers,Assay5)
S3method(JoinLayers,Seurat)
S3method(JoinLayers,StdAssay)
S3method(Key,"NULL")
S3method(Key,Assay)
S3method(Key,Assay5)
S3method(Key,DimReduc)
S3method(Key,KeyMixin)
S3method(Key,Seurat)
S3method(Key,SpatialImage)
S3method(Key,character)
S3method(Keys,FOV)
S3method(Keys,Seurat)
S3method(LayerData,Assay)
S3method(LayerData,Assay5)
S3method(LayerData,Seurat)
S3method(LayerData,StdAssay)
S3method(Layers,Assay)
S3method(Layers,Assay5)
S3method(Layers,Seurat)
S3method(Layers,StdAssay)
S3method(Loadings,DimReduc)
S3method(Loadings,Seurat)
S3method(MatchCells,"NULL")
S3method(MatchCells,character)
S3method(MatchCells,numeric)
S3method(Misc,Assay)
S3method(Misc,Assay5)
S3method(Misc,DimReduc)
S3method(Misc,Seurat)
S3method(Misc,StdAssay)
S3method(Molecules,FOV)
S3method(Project,Seurat)
S3method(Radius,Centroids)
S3method(Radius,SpatialImage)
S3method(RenameCells,Assay)
S3method(RenameCells,Assay5)
S3method(RenameCells,Centroids)
S3method(RenameCells,DimReduc)
S3method(RenameCells,FOV)
S3method(RenameCells,Neighbor)
S3method(RenameCells,Segmentation)
S3method(RenameCells,Seurat)
S3method(RenameCells,SpatialImage)
S3method(RenameCells,StdAssay)
S3method(RenameIdents,Seurat)
S3method(ReorderIdent,Seurat)
S3method(S4ToList,default)
S3method(S4ToList,list)
S3method(SVFInfo,Assay)
S3method(SVFInfo,Assay5)
S3method(SVFInfo,Seurat)
S3method(SVFInfo,StdAssay)
S3method(SetAssayData,Assay)
S3method(SetAssayData,Seurat)
S3method(SetAssayData,StdAssay)
S3method(SetIdent,Seurat)
S3method(Simplify,Molecules)
S3method(Simplify,Spatial)
S3method(SpatiallyVariableFeatures,Assay)
S3method(SpatiallyVariableFeatures,Assay5)
S3method(SpatiallyVariableFeatures,Seurat)
S3method(SpatiallyVariableFeatures,StdAssay)
S3method(StashIdent,Seurat)
S3method(Stdev,DimReduc)
S3method(Stdev,Seurat)
S3method(StitchMatrix,IterableMatrix)
S3method(StitchMatrix,default)
S3method(StitchMatrix,dgCMatrix)
S3method(StitchMatrix,matrix)
S3method(Theta,Centroids)
S3method(Tool,Seurat)
S3method(VariableFeatures,Assay)
S3method(VariableFeatures,Assay5)
S3method(VariableFeatures,Seurat)
S3method(VariableFeatures,StdAssay)
S3method(Version,Seurat)
S3method(WhichCells,Assay)
S3method(WhichCells,Assay5)
S3method(WhichCells,Seurat)
S3method(WhichCells,StdAssay)
S3method(aggregate,FOV)
S3method(aggregate,Molecules)
S3method(as.Centroids,Segmentation)
S3method(as.Graph,Matrix)
S3method(as.Graph,Neighbor)
S3method(as.Graph,matrix)
S3method(as.Neighbor,Graph)
S3method(as.Segmentation,Centroids)
S3method(as.list,SeuratCommand)
S3method(as.logical,JackStrawData)
S3method(as.matrix,LogMap)
S3method(as.sparse,Matrix)
S3method(as.sparse,data.frame)
S3method(as.sparse,matrix)
S3method(as.sparse,ngCMatrix)
S3method(dim,Assay)
S3method(dim,Assay5)
S3method(dim,DimReduc)
S3method(dim,FOV)
S3method(dim,Neighbor)
S3method(dim,Seurat)
S3method(dim,SpatialImage)
S3method(dim,StdAssay)
S3method(dimnames,Assay)
S3method(dimnames,Assay5)
S3method(dimnames,DimReduc)
S3method(dimnames,Seurat)
S3method(dimnames,StdAssay)
S3method(droplevels,LogMap)
S3method(droplevels,Seurat)
S3method(head,Assay)
S3method(head,Assay5)
S3method(head,Seurat)
S3method(head,StdAssay)
S3method(intersect,LogMap)
S3method(is.finite,Centroids)
S3method(is.infinite,Centroids)
S3method(labels,LogMap)
S3method(length,Centroids)
S3method(length,DimReduc)
S3method(length,FOV)
S3method(lengths,Centroids)
S3method(lengths,Segmentation)
S3method(levels,Seurat)
S3method(merge,Assay)
S3method(merge,Assay5)
S3method(merge,DimReduc)
S3method(merge,Seurat)
S3method(merge,StdAssay)
S3method(names,DimReduc)
S3method(names,FOV)
S3method(names,Seurat)
S3method(print,DimReduc)
S3method(split,Assay)
S3method(split,Assay5)
S3method(split,Seurat)
S3method(split,StdAssay)
S3method(subset,Assay)
S3method(subset,Assay5)
S3method(subset,Centroids)
S3method(subset,DimReduc)
S3method(subset,FOV)
S3method(subset,Molecules)
S3method(subset,Segmentation)
S3method(subset,Seurat)
S3method(subset,SpatialImage)
S3method(subset,StdAssay)
S3method(tail,Assay)
S3method(tail,Assay5)
S3method(tail,Seurat)
S3method(tail,StdAssay)
S3method(upgrade,seurat)
export("%!NA%")
export("%!na%")
export("%NA%")
export("%iff%")
export("%na%")
export("%||%")
export("DefaultAssay<-")
export("DefaultBoundary<-")
export("DefaultDimReduc<-")
export("DefaultFOV<-")
export("DefaultLayer<-")
export("Idents<-")
export("Index<-")
export("JS<-")
export("Key<-")
export("LayerData<-")
export("Loadings<-")
export("Misc<-")
export("Project<-")
export("Tool<-")
export("VariableFeatures<-")
export(.AssayClass)
export(.BPMatrixMode)
export(.CalcN)
export(.CheckFmargin)
export(.ClassPkg)
export(.Collections)
export(.Contains)
export(.CreateStdAssay)
export(.DefaultFOV)
export(.Deprecate)
export(.DiskLoad)
export(.FileMove)
export(.FilePath)
export(.FilterObjects)
export(.FindObject)
export(.GetMethod)
export(.IsFutureSeurat)
export(.KeyPattern)
export(.MARGIN)
export(.PropagateList)
export(.RandomKey)
export(.SparseSlots)
export(.Subobjects)
export(AddMetaData)
export(Assays)
export(AttachDeps)
export(Boundaries)
export(CastAssay)
export(Cells)
export(CellsByIdentities)
export(CheckDots)
export(CheckFeaturesNames)
export(CheckGC)
export(CheckLayersName)
export(CheckMatrix)
export(ClassKey)
export(Command)
export(CreateAssay5Object)
export(CreateAssayObject)
export(CreateCentroids)
export(CreateDimReducObject)
export(CreateFOV)
export(CreateMolecules)
export(CreateSegmentation)
export(CreateSeuratObject)
export(Crop)
export(DefaultAssay)
export(DefaultBoundary)
export(DefaultDimReduc)
export(DefaultFOV)
export(DefaultLayer)
export(Degrees)
export(Distances)
export(Embeddings)
export(EmptyDF)
export(EmptyMatrix)
export(ExtractField)
export(Features)
export(FetchData)
export(FilterObjects)
export(GetAssayData)
export(GetImage)
export(GetTissueCoordinates)
export(Graphs)
export(HVFInfo)
export(Idents)
export(Images)
export(Index)
export(Indices)
export(IsGlobal)
export(IsMatrixEmpty)
export(IsNamedList)
export(IsS4List)
export(IsSparse)
export(JS)
export(JoinLayers)
export(Key)
export(Keys)
export(LayerData)
export(Layers)
export(ListToS4)
export(LoadSeuratRds)
export(Loadings)
export(LogMap)
export(LogSeuratCommand)
export(MatchCells)
export(Misc)
export(Molecules)
export(Neighbors)
export(Overlay)
export(PackageCheck)
export(PolyVtx)
export(Project)
export(Radians)
export(Radius)
export(RandomName)
export(Reductions)
export(RegisterSparseMatrix)
export(RenameAssays)
export(RenameCells)
export(RenameIdents)
export(ReorderIdent)
export(RowMergeSparseMatrices)
export(S4ToList)
export(SVFInfo)
export(SaveSeuratRds)
export(SetAssayData)
export(SetIdent)
export(Simplify)
export(SparseEmptyMatrix)
export(SpatiallyVariableFeatures)
export(StashIdent)
export(Stdev)
export(StitchMatrix)
export(Theta)
export(Tool)
export(UpdateSeuratObject)
export(UpdateSlots)
export(VariableFeatures)
export(Version)
export(WhichCells)
export(as.Centroids)
export(as.Graph)
export(as.Neighbor)
export(as.Segmentation)
export(as.Seurat)
export(as.sparse)
export(handlers)
export(intersect)
export(plan)
export(t)
export(with_progress)
exportClasses(Assay)
exportClasses(Assay5)
exportClasses(DimReduc)
exportClasses(FOV)
exportClasses(Graph)
exportClasses(JackStrawData)
exportClasses(KeyMixin)
exportClasses(LogMap)
exportClasses(Neighbor)
exportClasses(Seurat)
exportClasses(SeuratCommand)
exportClasses(SpatialImage)
exportClasses(StdAssay)
exportMethods("[[")
exportMethods("[[<-")
exportMethods(Overlay)
exportMethods(colMeans)
exportMethods(colSums)
exportMethods(rowMeans)
exportMethods(rowSums)
exportMethods(show)
importClassesFrom(Matrix,CsparseMatrix)
importClassesFrom(Matrix,Matrix)
importClassesFrom(Matrix,RsparseMatrix)
importClassesFrom(Matrix,compMatrix)
importClassesFrom(Matrix,dMatrix)
importClassesFrom(Matrix,dgCMatrix)
importClassesFrom(Matrix,dsparseMatrix)
importClassesFrom(Matrix,generalMatrix)
importClassesFrom(Matrix,sparseMatrix)
importClassesFrom(sp,CRS)
importClassesFrom(sp,Spatial)
importClassesFrom(sp,SpatialPoints)
importClassesFrom(sp,SpatialPolygons)
importClassesFrom(spam,spam)
importFrom(Matrix,Matrix)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,nnzero)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,t)
importFrom(Rcpp,evalCpp)
importFrom(future,plan)
importFrom(future.apply,future_lapply)
importFrom(future.apply,future_mapply)
importFrom(generics,intersect)
importFrom(grDevices,as.raster)
importFrom(grid,nullGrob)
importFrom(lifecycle,deprecate_soft)
importFrom(lifecycle,deprecate_stop)
importFrom(lifecycle,deprecate_warn)
importFrom(lifecycle,deprecated)
importFrom(lifecycle,is_present)
importFrom(methods,"slot<-")
importFrom(methods,.hasSlot)
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,getClass)
importFrom(methods,getClassDef)
importFrom(methods,getClasses)
importFrom(methods,initialize)
importFrom(methods,is)
importFrom(methods,isClass)
importFrom(methods,isClassUnion)
importFrom(methods,isGeneric)
importFrom(methods,isXS3Class)
importFrom(methods,new)
importFrom(methods,selectMethod)
importFrom(methods,setAs)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setGeneric)
importFrom(methods,setMethod)
importFrom(methods,setOldClass)
importFrom(methods,setValidity)
importFrom(methods,show)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(methods,validObject)
importFrom(progressr,handlers)
importFrom(progressr,progressor)
importFrom(progressr,with_progress)
importFrom(rlang,"%||%")
importFrom(rlang,abort)
importFrom(rlang,arg_match)
importFrom(rlang,arg_match0)
importFrom(rlang,caller_env)
importFrom(rlang,check_installed)
importFrom(rlang,enquo)
importFrom(rlang,eval_tidy)
importFrom(rlang,have_name)
importFrom(rlang,inform)
importFrom(rlang,is_bare_character)
importFrom(rlang,is_bare_integerish)
importFrom(rlang,is_bare_list)
importFrom(rlang,is_bare_numeric)
importFrom(rlang,is_missing)
importFrom(rlang,is_na)
importFrom(rlang,is_named)
importFrom(rlang,is_null)
importFrom(rlang,is_quosure)
importFrom(rlang,is_scalar_character)
importFrom(rlang,missing_arg)
importFrom(rlang,ns_env_name)
importFrom(rlang,quo_get_env)
importFrom(rlang,quo_get_expr)
importFrom(rlang,warn)
importFrom(sp,CRS)
importFrom(sp,Polygon)
importFrom(sp,Polygons)
importFrom(sp,SpatialPoints)
importFrom(sp,SpatialPolygons)
importFrom(sp,bbox)
importFrom(sp,coordinates)
importFrom(sp,over)
importFrom(stats,aggregate)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,setNames)
importFrom(tools,file_path_sans_ext)
importFrom(utils,.DollarNames)
importFrom(utils,adist)
importFrom(utils,argsAnywhere)
importFrom(utils,getS3method)
importFrom(utils,head)
importFrom(utils,isS3method)
importFrom(utils,isS3stdGeneric)
importFrom(utils,methods)
importFrom(utils,modifyList)
importFrom(utils,packageVersion)
importFrom(utils,tail)
importFrom(utils,upgrade)
useDynLib(SeuratObject)
