# Generated by roxygen2: do not edit by hand

S3method("$",JackStrawData)
S3method("$",Seurat)
S3method("$",SeuratCommand)
S3method("$<-",Seurat)
S3method("DefaultAssay<-",DimReduc)
S3method("DefaultAssay<-",Seurat)
S3method("Idents<-",Seurat)
S3method("JS<-",DimReduc)
S3method("JS<-",JackStrawData)
S3method("Key<-",Assay)
S3method("Key<-",DimReduc)
S3method("Loadings<-",DimReduc)
S3method("Misc<-",Assay)
S3method("Misc<-",Seurat)
S3method("Project<-",Seurat)
S3method("Tool<-",Seurat)
S3method("VariableFeatures<-",Assay)
S3method("VariableFeatures<-",Seurat)
S3method("[",Assay)
S3method("[",DimReduc)
S3method("[",Seurat)
S3method("[",SeuratCommand)
S3method("[[",Assay)
S3method("[[",DimReduc)
S3method("[[",Seurat)
S3method("levels<-",Seurat)
S3method(.DollarNames,JackStrawData)
S3method(.DollarNames,Seurat)
S3method(.DollarNames,SeuratCommand)
S3method(AddMetaData,Assay)
S3method(AddMetaData,Seurat)
S3method(Cells,DimReduc)
S3method(Cells,default)
S3method(Command,Seurat)
S3method(DefaultAssay,DimReduc)
S3method(DefaultAssay,Seurat)
S3method(Embeddings,DimReduc)
S3method(Embeddings,Seurat)
S3method(FindClusters,Seurat)
S3method(FindClusters,default)
S3method(FindMarkers,Seurat)
S3method(FindMarkers,default)
S3method(FindNeighbors,Assay)
S3method(FindNeighbors,Seurat)
S3method(FindNeighbors,default)
S3method(FindNeighbors,dist)
S3method(FindVariableFeatures,Assay)
S3method(FindVariableFeatures,Seurat)
S3method(FindVariableFeatures,default)
S3method(GetAssay,Seurat)
S3method(GetAssayData,Assay)
S3method(GetAssayData,Seurat)
S3method(HVFInfo,Assay)
S3method(HVFInfo,Seurat)
S3method(Idents,Seurat)
S3method(JS,DimReduc)
S3method(JS,JackStrawData)
S3method(Key,Assay)
S3method(Key,DimReduc)
S3method(Key,Seurat)
S3method(Loadings,DimReduc)
S3method(Loadings,Seurat)
S3method(Misc,Assay)
S3method(Misc,Seurat)
S3method(NormalizeData,Assay)
S3method(NormalizeData,Seurat)
S3method(NormalizeData,default)
S3method(OldWhichCells,Assay)
S3method(OldWhichCells,Seurat)
S3method(Project,Seurat)
S3method(ReadH5AD,H5File)
S3method(ReadH5AD,character)
S3method(RenameCells,Assay)
S3method(RenameCells,DimReduc)
S3method(RenameCells,Seurat)
S3method(RenameIdents,Seurat)
S3method(ReorderIdent,Seurat)
S3method(RunALRA,Seurat)
S3method(RunALRA,default)
S3method(RunCCA,Seurat)
S3method(RunCCA,default)
S3method(RunICA,Assay)
S3method(RunICA,Seurat)
S3method(RunICA,default)
S3method(RunLSI,Assay)
S3method(RunLSI,Seurat)
S3method(RunLSI,default)
S3method(RunPCA,Assay)
S3method(RunPCA,Seurat)
S3method(RunPCA,default)
S3method(RunTSNE,DimReduc)
S3method(RunTSNE,Seurat)
S3method(RunTSNE,dist)
S3method(RunTSNE,matrix)
S3method(RunUMAP,Graph)
S3method(RunUMAP,Seurat)
S3method(RunUMAP,default)
S3method(ScaleData,Assay)
S3method(ScaleData,Seurat)
S3method(ScaleData,default)
S3method(ScoreJackStraw,DimReduc)
S3method(ScoreJackStraw,JackStrawData)
S3method(ScoreJackStraw,Seurat)
S3method(SetAssayData,Assay)
S3method(SetAssayData,Seurat)
S3method(SetIdent,Seurat)
S3method(StashIdent,Seurat)
S3method(Stdev,DimReduc)
S3method(Stdev,Seurat)
S3method(SubsetData,Assay)
S3method(SubsetData,Seurat)
S3method(Tool,Seurat)
S3method(VariableFeatures,Assay)
S3method(VariableFeatures,Seurat)
S3method(WhichCells,Assay)
S3method(WhichCells,Seurat)
S3method(WriteH5AD,Seurat)
S3method(as.Graph,Matrix)
S3method(as.Graph,matrix)
S3method(as.Seurat,SingleCellExperiment)
S3method(as.Seurat,loom)
S3method(as.SingleCellExperiment,Seurat)
S3method(as.data.frame,Matrix)
S3method(as.logical,JackStrawData)
S3method(as.loom,Seurat)
S3method(as.sparse,H5Group)
S3method(as.sparse,Matrix)
S3method(as.sparse,data.frame)
S3method(as.sparse,matrix)
S3method(dim,Assay)
S3method(dim,DimReduc)
S3method(dim,Seurat)
S3method(dimnames,Assay)
S3method(dimnames,DimReduc)
S3method(dimnames,Seurat)
S3method(droplevels,Seurat)
S3method(length,DimReduc)
S3method(levels,Seurat)
S3method(merge,Assay)
S3method(merge,Seurat)
S3method(names,DimReduc)
S3method(names,Seurat)
S3method(print,DimReduc)
S3method(subset,Assay)
S3method(subset,DimReduc)
S3method(subset,Seurat)
export("DefaultAssay<-")
export("Idents<-")
export("JS<-")
export("Key<-")
export("Loadings<-")
export("Misc<-")
export("Project<-")
export("Tool<-")
export("VariableFeatures<-")
export(ALRAChooseKPlot)
export(AddMetaData)
export(AddModuleScore)
export(AugmentPlot)
export(AverageExpression)
export(BarcodeInflectionsPlot)
export(BlackAndWhite)
export(BlueAndRed)
export(BoldTitle)
export(BuildClusterTree)
export(CalculateBarcodeInflections)
export(CaseMatch)
export(CellCycleScoring)
export(CellScatter)
export(CellSelector)
export(Cells)
export(CollapseSpeciesExpressionMatrix)
export(CombinePlots)
export(Command)
export(CreateAssayObject)
export(CreateDimReducObject)
export(CreateGeneActivityMatrix)
export(CreateSeuratObject)
export(CustomDistance)
export(CustomPalette)
export(DarkTheme)
export(DefaultAssay)
export(DietSeurat)
export(DimHeatmap)
export(DimPlot)
export(DoHeatmap)
export(DotPlot)
export(ElbowPlot)
export(Embeddings)
export(ExpMean)
export(ExpSD)
export(ExpVar)
export(ExportToCellbrowser)
export(FeatureLocator)
export(FeaturePlot)
export(FeatureScatter)
export(FetchData)
export(FindAllMarkers)
export(FindClusters)
export(FindConservedMarkers)
export(FindIntegrationAnchors)
export(FindMarkers)
export(FindNeighbors)
export(FindTransferAnchors)
export(FindVariableFeatures)
export(FontSize)
export(GetAssay)
export(GetAssayData)
export(GetIntegrationData)
export(HTODemux)
export(HTOHeatmap)
export(HVFInfo)
export(HoverLocator)
export(Idents)
export(IntegrateData)
export(JS)
export(JackStraw)
export(JackStrawPlot)
export(Key)
export(L2CCA)
export(L2Dim)
export(LabelClusters)
export(LabelPoints)
export(Loadings)
export(LocalStruct)
export(LogNormalize)
export(LogSeuratCommand)
export(LogVMR)
export(MULTIseqDemux)
export(MetaFeature)
export(MinMax)
export(Misc)
export(MixingMetric)
export(NoAxes)
export(NoGrid)
export(NoLegend)
export(NormalizeData)
export(OldWhichCells)
export(PCAPlot)
export(PCASigGenes)
export(PCHeatmap)
export(PercentageFeatureSet)
export(PlotClusterTree)
export(PolyDimPlot)
export(PolyFeaturePlot)
export(Project)
export(ProjectDim)
export(PurpleAndYellow)
export(Read10X)
export(Read10X_h5)
export(ReadAlevin)
export(ReadAlevinCsv)
export(ReadH5AD)
export(RelativeCounts)
export(RenameCells)
export(RenameIdents)
export(ReorderIdent)
export(RestoreLegend)
export(RidgePlot)
export(RotatedAxis)
export(RunALRA)
export(RunCCA)
export(RunICA)
export(RunLSI)
export(RunPCA)
export(RunTSNE)
export(RunUMAP)
export(SCTransform)
export(SampleUMI)
export(ScaleData)
export(ScoreJackStraw)
export(SelectIntegrationFeatures)
export(SetAssayData)
export(SetIdent)
export(SetIntegrationData)
export(SeuratAxes)
export(SeuratTheme)
export(SpatialTheme)
export(SplitObject)
export(StashIdent)
export(Stdev)
export(StopCellbrowser)
export(SubsetByBarcodeInflections)
export(SubsetData)
export(TF.IDF)
export(TSNEPlot)
export(Tool)
export(TopCells)
export(TopFeatures)
export(TransferData)
export(UMAPPlot)
export(UpdateSeuratObject)
export(VariableFeaturePlot)
export(VariableFeatures)
export(VizDimLoadings)
export(VlnPlot)
export(WhichCells)
export(WhiteBackground)
export(as.Graph)
export(as.Seurat)
export(as.SingleCellExperiment)
export(as.loom)
export(as.sparse)
exportClasses(AnchorSet)
exportClasses(Assay)
exportClasses(DimReduc)
exportClasses(Graph)
exportClasses(IntegrationData)
exportClasses(JackStrawData)
exportClasses(Seurat)
exportClasses(SeuratCommand)
import(Matrix)
importClassesFrom(Matrix,dgCMatrix)
importFrom(KernSmooth,bkde)
importFrom(MASS,glm.nb)
importFrom(MASS,kde2d)
importFrom(Matrix,Matrix)
importFrom(Matrix,as.matrix)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,readMM)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(RANN,nn2)
importFrom(RColorBrewer,brewer.pal.info)
importFrom(ROCR,performance)
importFrom(ROCR,prediction)
importFrom(Rcpp,evalCpp)
importFrom(Rtsne,Rtsne)
importFrom(SDMTools,pnt.in.poly)
importFrom(ape,as.phylo)
importFrom(ape,drop.tip)
importFrom(ape,nodelabels)
importFrom(ape,plot.phylo)
importFrom(cluster,clara)
importFrom(cowplot,get_legend)
importFrom(cowplot,plot_grid)
importFrom(cowplot,theme_cowplot)
importFrom(fitdistrplus,fitdist)
importFrom(future,plan)
importFrom(future.apply,future_apply)
importFrom(future.apply,future_lapply)
importFrom(future.apply,future_sapply)
importFrom(ggplot2,GeomPolygon)
importFrom(ggplot2,GeomViolin)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,annotation_raster)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,cut_number)
importFrom(ggplot2,dup_axis)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_blank)
importFrom(ggplot2,geom_jitter)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_brewer)
importFrom(ggplot2,scale_color_distiller)
importFrom(ggplot2,scale_color_gradient)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_identity)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_fill_viridis_c)
importFrom(ggplot2,scale_radius)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,stat_density2d)
importFrom(ggplot2,stat_qq)
importFrom(ggplot2,sym)
importFrom(ggplot2,theme)
importFrom(ggplot2,vars)
importFrom(ggplot2,waiver)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_text_repel)
importFrom(ggridges,geom_density_ridges)
importFrom(ggridges,theme_ridges)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,rgb)
importFrom(graphics,axis)
importFrom(graphics,locator)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,plot.new)
importFrom(graphics,smoothScatter)
importFrom(grid,grobName)
importFrom(grid,grobTree)
importFrom(grid,unit)
importFrom(ica,icafast)
importFrom(ica,icaimax)
importFrom(ica,icajade)
importFrom(igraph,E)
importFrom(igraph,graph.adjacency)
importFrom(igraph,plot.igraph)
importFrom(irlba,irlba)
importFrom(lmtest,lrtest)
importFrom(metap,minimump)
importFrom(methods,"slot<-")
importFrom(methods,.hasSlot)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,setClassUnion)
importFrom(methods,setMethod)
importFrom(methods,setOldClass)
importFrom(methods,signature)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(pbapply,pbapply)
importFrom(pbapply,pblapply)
importFrom(pbapply,pbsapply)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(png,readPNG)
importFrom(reticulate,dict)
importFrom(reticulate,import)
importFrom(reticulate,np_array)
importFrom(reticulate,py_module_available)
importFrom(reticulate,py_set_seed)
importFrom(reticulate,r_to_py)
importFrom(reticulate,tuple)
importFrom(rlang,"!!")
importFrom(rsvd,rsvd)
importFrom(scales,hue_pal)
importFrom(scales,zero_range)
importFrom(sctransform,correct_counts)
importFrom(sctransform,get_residual_var)
importFrom(sctransform,get_residuals)
importFrom(sctransform,vst)
importFrom(stats,aggregate)
importFrom(stats,anova)
importFrom(stats,approxfun)
importFrom(stats,as.dist)
importFrom(stats,as.formula)
importFrom(stats,ave)
importFrom(stats,coef)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,glm)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,lm)
importFrom(stats,loess)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,pnbinom)
importFrom(stats,pnorm)
importFrom(stats,poisson)
importFrom(stats,prcomp)
importFrom(stats,prop.test)
importFrom(stats,quantile)
importFrom(stats,qunif)
importFrom(stats,relevel)
importFrom(stats,residuals)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(tsne,tsne)
importFrom(utils,.DollarNames)
importFrom(utils,argsAnywhere)
importFrom(utils,browseURL)
importFrom(utils,file_test)
importFrom(utils,getAnywhere)
importFrom(utils,globalVariables)
importFrom(utils,packageVersion)
importFrom(utils,read.csv)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,write.table)
useDynLib(Seurat)
