# Generated by roxygen2: do not edit by hand S3method("$",JackStrawData) S3method("$",Seurat) S3method("$",SeuratCommand) S3method("$<-",Seurat) S3method("DefaultAssay<-",Assay) S3method("DefaultAssay<-",DimReduc) S3method("DefaultAssay<-",Graph) S3method("DefaultAssay<-",Seurat) S3method("DefaultAssay<-",SpatialImage) S3method("Idents<-",Seurat) S3method("Index<-",Neighbor) S3method("JS<-",DimReduc) S3method("JS<-",JackStrawData) S3method("Key<-",Assay) S3method("Key<-",DimReduc) S3method("Key<-",SpatialImage) S3method("Loadings<-",DimReduc) S3method("Misc<-",Assay) S3method("Misc<-",DimReduc) S3method("Misc<-",Seurat) S3method("Project<-",Seurat) S3method("Tool<-",Seurat) S3method("VariableFeatures<-",Assay) S3method("VariableFeatures<-",Seurat) S3method("[",Assay) S3method("[",DimReduc) S3method("[",Seurat) S3method("[",SeuratCommand) S3method("[",SlideSeq) S3method("[",SpatialImage) S3method("[",VisiumV1) S3method("[[",Assay) S3method("[[",DimReduc) S3method("[[",Seurat) S3method("dimnames<-",Assay) S3method("levels<-",Seurat) S3method(.DollarNames,JackStrawData) S3method(.DollarNames,Seurat) S3method(.DollarNames,SeuratCommand) S3method(AddMetaData,Assay) S3method(AddMetaData,Seurat) S3method(Cells,DimReduc) S3method(Cells,Neighbor) S3method(Cells,STARmap) S3method(Cells,SlideSeq) S3method(Cells,SpatialImage) S3method(Cells,VisiumV1) S3method(Cells,default) S3method(Command,Seurat) S3method(CreateSeuratObject,Assay) S3method(CreateSeuratObject,default) S3method(DefaultAssay,Assay) S3method(DefaultAssay,DimReduc) S3method(DefaultAssay,Graph) S3method(DefaultAssay,Seurat) S3method(DefaultAssay,SeuratCommand) S3method(DefaultAssay,SpatialImage) S3method(Distances,Neighbor) S3method(Embeddings,DimReduc) S3method(Embeddings,Seurat) S3method(FindClusters,Seurat) S3method(FindClusters,default) S3method(FindMarkers,Assay) S3method(FindMarkers,DimReduc) S3method(FindMarkers,Seurat) S3method(FindMarkers,default) S3method(FindNeighbors,Assay) S3method(FindNeighbors,Seurat) S3method(FindNeighbors,default) S3method(FindNeighbors,dist) S3method(FindSpatiallyVariableFeatures,Assay) S3method(FindSpatiallyVariableFeatures,Seurat) S3method(FindSpatiallyVariableFeatures,default) S3method(FindVariableFeatures,Assay) S3method(FindVariableFeatures,Seurat) S3method(FindVariableFeatures,default) S3method(FoldChange,Assay) S3method(FoldChange,DimReduc) S3method(FoldChange,Seurat) S3method(FoldChange,default) S3method(GetAssay,Seurat) S3method(GetAssayData,Assay) S3method(GetAssayData,Seurat) S3method(GetImage,STARmap) S3method(GetImage,Seurat) S3method(GetImage,SlideSeq) S3method(GetImage,SpatialImage) S3method(GetImage,VisiumV1) S3method(GetTissueCoordinates,STARmap) S3method(GetTissueCoordinates,Seurat) S3method(GetTissueCoordinates,SlideSeq) S3method(GetTissueCoordinates,SpatialImage) S3method(GetTissueCoordinates,VisiumV1) S3method(HVFInfo,Assay) S3method(HVFInfo,Seurat) S3method(Idents,Seurat) S3method(Index,Neighbor) S3method(Indices,Neighbor) S3method(IntegrateEmbeddings,IntegrationAnchorSet) S3method(IntegrateEmbeddings,TransferAnchorSet) S3method(IsGlobal,DimReduc) S3method(IsGlobal,SpatialImage) S3method(IsGlobal,default) S3method(JS,DimReduc) S3method(JS,JackStrawData) S3method(Key,Assay) S3method(Key,DimReduc) S3method(Key,Seurat) S3method(Key,SpatialImage) S3method(Loadings,DimReduc) S3method(Loadings,Seurat) S3method(MappingScore,AnchorSet) S3method(MappingScore,default) S3method(Misc,Assay) S3method(Misc,DimReduc) S3method(Misc,Seurat) S3method(NormalizeData,Assay) S3method(NormalizeData,Seurat) S3method(NormalizeData,default) S3method(OldWhichCells,Assay) S3method(OldWhichCells,Seurat) S3method(Project,Seurat) S3method(ProjectUMAP,DimReduc) S3method(ProjectUMAP,Seurat) S3method(ProjectUMAP,default) S3method(Radius,STARmap) S3method(Radius,SlideSeq) S3method(Radius,SpatialImage) S3method(Radius,VisiumV1) S3method(ReadH5AD,H5File) S3method(ReadH5AD,character) S3method(RenameCells,Assay) S3method(RenameCells,DimReduc) S3method(RenameCells,Neighbor) S3method(RenameCells,STARmap) S3method(RenameCells,Seurat) S3method(RenameCells,SlideSeq) S3method(RenameCells,SpatialImage) S3method(RenameCells,VisiumV1) 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(RunLDA,Assay) S3method(RunLDA,Seurat) S3method(RunLDA,default) S3method(RunPCA,Assay) S3method(RunPCA,Seurat) S3method(RunPCA,default) S3method(RunSPCA,Assay) S3method(RunSPCA,Seurat) S3method(RunSPCA,default) S3method(RunTSNE,DimReduc) S3method(RunTSNE,Seurat) S3method(RunTSNE,dist) S3method(RunTSNE,matrix) S3method(RunUMAP,Graph) S3method(RunUMAP,Neighbor) S3method(RunUMAP,Seurat) S3method(RunUMAP,default) S3method(SVFInfo,Assay) S3method(SVFInfo,Seurat) S3method(ScaleData,Assay) S3method(ScaleData,Seurat) S3method(ScaleData,default) S3method(ScaleFactors,VisiumV1) S3method(ScoreJackStraw,DimReduc) S3method(ScoreJackStraw,JackStrawData) S3method(ScoreJackStraw,Seurat) S3method(SetAssayData,Assay) S3method(SetAssayData,Seurat) S3method(SetIdent,Seurat) S3method(SpatiallyVariableFeatures,Assay) S3method(SpatiallyVariableFeatures,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.CellDataSet,Seurat) S3method(as.Graph,Matrix) S3method(as.Graph,Neighbor) S3method(as.Graph,matrix) S3method(as.Neighbor,Graph) S3method(as.Seurat,CellDataSet) S3method(as.Seurat,SingleCellExperiment) S3method(as.Seurat,loom) S3method(as.SingleCellExperiment,Seurat) S3method(as.data.frame,Matrix) S3method(as.list,SeuratCommand) 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,Neighbor) S3method(dim,STARmap) S3method(dim,Seurat) S3method(dim,SlideSeq) S3method(dim,SpatialImage) S3method(dim,VisiumV1) S3method(dimnames,Assay) S3method(dimnames,DimReduc) S3method(dimnames,Seurat) S3method(droplevels,Seurat) S3method(length,DimReduc) S3method(levels,Seurat) S3method(merge,Assay) S3method(merge,DimReduc) S3method(merge,Seurat) S3method(names,DimReduc) S3method(names,Seurat) S3method(print,DimReduc) S3method(subset,Assay) S3method(subset,DimReduc) S3method(subset,STARmap) S3method(subset,Seurat) S3method(subset,SlideSeq) S3method(subset,SpatialImage) S3method(subset,VisiumV1) export("DefaultAssay<-") export("Idents<-") export("Index<-") export("JS<-") export("Key<-") export("Loadings<-") export("Misc<-") export("Project<-") export("Tool<-") export("VariableFeatures<-") export(ALRAChooseKPlot) export(AddMetaData) export(AddModuleScore) export(Assays) export(AugmentPlot) export(AverageExpression) export(BGTextColor) export(BarcodeInflectionsPlot) export(BlackAndWhite) export(BlueAndRed) export(BoldTitle) export(BuildClusterTree) export(CalcPerturbSig) export(CalculateBarcodeInflections) export(CaseMatch) export(CellCycleScoring) export(CellScatter) export(CellSelector) export(Cells) export(CellsByIdentities) export(CenterTitle) export(CollapseEmbeddingOutliers) export(CollapseSpeciesExpressionMatrix) export(ColorDimSplit) export(CombinePlots) export(Command) export(CreateAssayObject) export(CreateDimReducObject) export(CreateSeuratObject) export(CustomDistance) export(CustomPalette) export(DEenrichRPlot) export(DarkTheme) export(DefaultAssay) export(DietSeurat) export(DimHeatmap) export(DimPlot) export(DiscretePalette) export(Distances) export(DoHeatmap) export(DotPlot) export(ElbowPlot) export(Embeddings) export(ExpMean) export(ExpSD) export(ExpVar) export(ExportToCellbrowser) export(FastRowScale) export(FeatureLocator) export(FeaturePlot) export(FeatureScatter) export(FetchData) export(FilterSlideSeq) export(FindAllMarkers) export(FindClusters) export(FindConservedMarkers) export(FindIntegrationAnchors) export(FindMarkers) export(FindMultiModalNeighbors) export(FindNeighbors) export(FindSpatiallyVariableFeatures) export(FindSubCluster) export(FindTransferAnchors) export(FindVariableFeatures) export(FoldChange) export(FontSize) export(GeneSymbolThesarus) export(GetAssay) export(GetAssayData) export(GetImage) export(GetIntegrationData) export(GetResidual) export(GetTissueCoordinates) export(GetTransferPredictions) export(Graphs) export(GroupCorrelation) export(GroupCorrelationPlot) export(HTODemux) export(HTOHeatmap) export(HVFInfo) export(HoverLocator) export(IFeaturePlot) export(ISpatialDimPlot) export(ISpatialFeaturePlot) export(Idents) export(Images) export(Index) export(Indices) export(IntegrateData) export(IntegrateEmbeddings) export(Intensity) export(IsGlobal) export(JS) export(JackStraw) export(JackStrawPlot) export(Key) export(L2CCA) export(L2Dim) export(LabelClusters) export(LabelPoints) export(LinkedDimPlot) export(LinkedFeaturePlot) export(Load10X_Spatial) export(LoadAnnoyIndex) export(LoadSTARmap) export(Loadings) export(LocalStruct) export(LogNormalize) export(LogSeuratCommand) export(LogVMR) export(Luminance) export(MULTIseqDemux) export(MapQuery) export(MappingScore) export(MetaFeature) export(MinMax) export(Misc) export(MixingMetric) export(MixscapeHeatmap) export(MixscapeLDA) export(NNPlot) export(Neighbors) export(NoAxes) export(NoGrid) export(NoLegend) export(NormalizeData) export(OldWhichCells) export(PCAPlot) export(PCASigGenes) export(PCHeatmap) export(PercentageFeatureSet) export(PlotClusterTree) export(PlotPerturbScore) export(PolyDimPlot) export(PolyFeaturePlot) export(PredictAssay) export(PrepLDA) export(PrepSCTIntegration) export(Project) export(ProjectDim) export(ProjectUMAP) export(PurpleAndYellow) export(Radius) export(Read10X) export(Read10X_Image) export(Read10X_h5) export(ReadAlevin) export(ReadAlevinCsv) export(ReadH5AD) export(ReadSlideSeq) export(Reductions) export(RegroupIdents) export(RelativeCounts) export(RenameAssays) export(RenameCells) export(RenameIdents) export(ReorderIdent) export(RestoreLegend) export(RidgePlot) export(RotatedAxis) export(RowMergeSparseMatrices) export(RunALRA) export(RunCCA) export(RunICA) export(RunLDA) export(RunMarkVario) export(RunMixscape) export(RunMoransI) export(RunPCA) export(RunSPCA) export(RunTSNE) export(RunUMAP) export(SCTransform) export(SVFInfo) export(SampleUMI) export(SaveAnnoyIndex) export(ScaleData) export(ScaleFactors) export(ScoreJackStraw) export(SelectIntegrationFeatures) export(SetAssayData) export(SetIdent) export(SetIntegrationData) export(SeuratAxes) export(SeuratTheme) export(SpatialDimPlot) export(SpatialFeaturePlot) export(SpatialPlot) export(SpatialTheme) export(SpatiallyVariableFeatures) export(SplitObject) export(StashIdent) export(Stdev) export(StopCellbrowser) export(SubsetByBarcodeInflections) export(SubsetData) export(TF.IDF) export(TSNEPlot) export(Tool) export(TopCells) export(TopFeatures) export(TopNeighbors) export(TransferData) export(UMAPPlot) export(UpdateSeuratObject) export(UpdateSymbolList) export(VariableFeaturePlot) export(VariableFeatures) export(VizDimLoadings) export(VlnPlot) export(WhichCells) export(WhiteBackground) export(as.CellDataSet) export(as.Graph) export(as.Neighbor) export(as.Seurat) export(as.SingleCellExperiment) export(as.loom) export(as.sparse) export(scalefactors) exportClasses(AnchorSet) exportClasses(Assay) exportClasses(DimReduc) exportClasses(Graph) exportClasses(IntegrationAnchorSet) exportClasses(IntegrationData) exportClasses(JackStrawData) exportClasses(ModalityWeights) exportClasses(Neighbor) exportClasses(Seurat) exportClasses(SeuratCommand) exportClasses(SpatialImage) exportClasses(TransferAnchorSet) exportClasses(VisiumV1) import(Matrix) importClassesFrom(Matrix,dgCMatrix) importFrom(KernSmooth,bkde) importFrom(MASS,glm.nb) importFrom(MASS,lda) 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) importFrom(RColorBrewer,brewer.pal.info) importFrom(ROCR,performance) importFrom(ROCR,prediction) importFrom(Rcpp,evalCpp) importFrom(RcppAnnoy,AnnoyAngular) importFrom(RcppAnnoy,AnnoyEuclidean) importFrom(RcppAnnoy,AnnoyHamming) importFrom(RcppAnnoy,AnnoyManhattan) importFrom(Rtsne,Rtsne) importFrom(cluster,clara) importFrom(cowplot,get_legend) importFrom(cowplot,plot_grid) importFrom(cowplot,theme_cowplot) importFrom(fitdistrplus,fitdist) importFrom(future,nbrOfWorkers) importFrom(future,plan) importFrom(future.apply,future_lapply) importFrom(future.apply,future_sapply) importFrom(ggplot2,Geom) importFrom(ggplot2,GeomPolygon) importFrom(ggplot2,GeomViolin) importFrom(ggplot2,aes) importFrom(ggplot2,aes_string) importFrom(ggplot2,alpha) importFrom(ggplot2,annotation_raster) importFrom(ggplot2,coord_cartesian) importFrom(ggplot2,coord_fixed) importFrom(ggplot2,coord_flip) importFrom(ggplot2,cut_number) importFrom(ggplot2,discrete_scale) importFrom(ggplot2,draw_key_point) importFrom(ggplot2,dup_axis) importFrom(ggplot2,element_blank) importFrom(ggplot2,element_line) importFrom(ggplot2,element_rect) importFrom(ggplot2,element_text) importFrom(ggplot2,facet_grid) importFrom(ggplot2,facet_wrap) importFrom(ggplot2,geom_abline) importFrom(ggplot2,geom_bar) importFrom(ggplot2,geom_blank) importFrom(ggplot2,geom_boxplot) importFrom(ggplot2,geom_density) importFrom(ggplot2,geom_hline) importFrom(ggplot2,geom_jitter) importFrom(ggplot2,geom_label) importFrom(ggplot2,geom_line) importFrom(ggplot2,geom_point) importFrom(ggplot2,geom_polygon) importFrom(ggplot2,geom_raster) importFrom(ggplot2,geom_rect) 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,ggproto_parent) 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,position_dodge) importFrom(ggplot2,position_jitterdodge) importFrom(ggplot2,scale_alpha) importFrom(ggplot2,scale_alpha_ordinal) 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_brewer) 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,theme_classic) importFrom(ggplot2,theme_void) importFrom(ggplot2,transform_position) importFrom(ggplot2,unit) importFrom(ggplot2,vars) importFrom(ggplot2,waiver) importFrom(ggplot2,xlab) importFrom(ggplot2,xlim) importFrom(ggplot2,ylab) importFrom(ggplot2,ylim) importFrom(ggrepel,geom_label_repel) importFrom(ggrepel,geom_text_repel) importFrom(ggridges,geom_density_ridges) importFrom(ggridges,theme_ridges) importFrom(grDevices,as.raster) 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,addGrob) importFrom(grid,editGrob) importFrom(grid,gTree) importFrom(grid,gpar) importFrom(grid,grobName) importFrom(grid,grobTree) importFrom(grid,nullGrob) importFrom(grid,pointsGrob) importFrom(grid,rasterGrob) importFrom(grid,unit) importFrom(grid,viewport) importFrom(httr,GET) importFrom(httr,accept_json) importFrom(httr,content) importFrom(httr,status_code) importFrom(httr,timeout) importFrom(ica,icafast) importFrom(ica,icaimax) importFrom(ica,icajade) importFrom(igraph,E) importFrom(igraph,graph.adjacency) importFrom(igraph,graph_from_adj_list) importFrom(igraph,graph_from_adjacency_matrix) importFrom(igraph,plot.igraph) importFrom(irlba,irlba) importFrom(jsonlite,fromJSON) importFrom(leiden,leiden) importFrom(lmtest,lrtest) importFrom(matrixStats,rowMeans2) importFrom(matrixStats,rowSds) importFrom(matrixStats,rowSums2) 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(miniUI,gadgetTitleBar) importFrom(miniUI,miniButtonBlock) importFrom(miniUI,miniContentPanel) importFrom(miniUI,miniPage) importFrom(miniUI,miniTitleBarButton) importFrom(patchwork,wrap_plots) importFrom(pbapply,pbapply) importFrom(pbapply,pblapply) importFrom(pbapply,pbsapply) importFrom(plotly,add_annotations) importFrom(plotly,layout) importFrom(plotly,plot_ly) importFrom(plotly,raster2uri) 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,tuple) importFrom(rlang,"!!") importFrom(rlang,enquo) importFrom(rlang,eval_tidy) importFrom(rlang,is_quosure) importFrom(rsvd,rsvd) importFrom(scales,brewer_pal) importFrom(scales,hue_pal) importFrom(scales,rescale) importFrom(scales,squish_infinite) importFrom(scales,zero_range) importFrom(sctransform,correct_counts) importFrom(sctransform,get_residual_var) importFrom(sctransform,get_residuals) importFrom(sctransform,vst) importFrom(shiny,brushOpts) importFrom(shiny,brushedPoints) importFrom(shiny,clickOpts) importFrom(shiny,fillRow) importFrom(shiny,hoverOpts) importFrom(shiny,nearPoints) importFrom(shiny,observe) importFrom(shiny,observeEvent) importFrom(shiny,plotOutput) importFrom(shiny,reactiveValues) importFrom(shiny,renderPlot) importFrom(shiny,renderPrint) importFrom(shiny,runGadget) importFrom(shiny,selectInput) importFrom(shiny,sidebarPanel) importFrom(shiny,sliderInput) importFrom(shiny,stopApp) importFrom(shiny,updateSelectInput) importFrom(shiny,verbatimTextOutput) importFrom(spatstat,markvario) importFrom(spatstat,ppp) 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,complete.cases) 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,poisson) importFrom(stats,prcomp) importFrom(stats,predict) 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(tibble,tibble) importFrom(tools,file_ext) importFrom(tools,file_path_sans_ext) importFrom(utils,.DollarNames) importFrom(utils,argsAnywhere) importFrom(utils,browseURL) importFrom(utils,capture.output) importFrom(utils,file_test) importFrom(utils,globalVariables) importFrom(utils,isS3method) importFrom(utils,isS3stdGeneric) importFrom(utils,methods) 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) importFrom(uwot,umap) importFrom(uwot,umap_transform) useDynLib(Seurat)