NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(RunDM,Neighbor)
S3method(RunDM,Seurat)
S3method(RunDM,matrix)
S3method(RunFR,Seurat)
S3method(RunFR,default)
S3method(RunGLMPCA,Assay)
S3method(RunGLMPCA,Seurat)
S3method(RunGLMPCA,default)
S3method(RunHarmony2,Seurat)
S3method(RunLargeVis,Seurat)
S3method(RunLargeVis,default)
S3method(RunMDS,Assay)
S3method(RunMDS,Seurat)
S3method(RunMDS,default)
S3method(RunNMF,Assay)
S3method(RunNMF,Seurat)
S3method(RunNMF,default)
S3method(RunPHATE,Seurat)
S3method(RunPHATE,default)
S3method(RunPaCMAP,Seurat)
S3method(RunPaCMAP,default)
S3method(RunTriMap,Seurat)
S3method(RunTriMap,default)
S3method(RunUMAP2,Seurat)
S3method(RunUMAP2,default)
S3method(drop_data,default)
S3method(drop_data,ggplot)
S3method(drop_data,patchwork)
S3method(slim_data,default)
S3method(slim_data,ggplot)
S3method(slim_data,patchwork)
export(AnnotateFeatures)
export(BBKNN_integrate)
export(CC_GenePrefetch)
export(CSS_integrate)
export(CellCorHeatmap)
export(CellDensityPlot)
export(CellDimPlot)
export(CellDimPlot3D)
export(CellScoring)
export(CellStatPlot)
export(ComBat_integrate)
export(Conos_integrate)
export(CreateDataFile)
export(CreateMetaFile)
export(DefaultReduction)
export(DynamicHeatmap)
export(DynamicPlot)
export(EnrichmentPlot)
export(FeatureCorPlot)
export(FeatureDimPlot)
export(FeatureDimPlot3D)
export(FeatureHeatmap)
export(FeatureStatPlot)
export(FetchH5)
export(GSEAPlot)
export(GeneConvert)
export(GraphPlot)
export(GroupHeatmap)
export(Harmony_integrate)
export(Integration_SCP)
export(LIGER_integrate)
export(LineagePlot)
export(ListDB)
export(MNN_integrate)
export(PAGAPlot)
export(PrepareDB)
export(PrepareEnv)
export(PrepareSCExplorer)
export(ProjectionPlot)
export(RecoverCounts)
export(RenameClusters)
export(RenameFeatures)
export(RunCSSMap)
export(RunCellQC)
export(RunDEtest)
export(RunDM)
export(RunDimReduction)
export(RunDoubletCalling)
export(RunDynamicEnrichment)
export(RunDynamicFeatures)
export(RunEnrichment)
export(RunFR)
export(RunGLMPCA)
export(RunGSEA)
export(RunHarmony2)
export(RunKNNMap)
export(RunKNNPredict)
export(RunLargeVis)
export(RunMDS)
export(RunMonocle2)
export(RunMonocle3)
export(RunNMF)
export(RunPAGA)
export(RunPCAMap)
export(RunPHATE)
export(RunPaCMAP)
export(RunPalantir)
export(RunSCExplorer)
export(RunSCVELO)
export(RunScmap)
export(RunSeuratMap)
export(RunSingleR)
export(RunSlingshot)
export(RunSymphonyMap)
export(RunTriMap)
export(RunUMAP2)
export(RunWOT)
export(SankeyPlot)
export(Scanorama_integrate)
export(Seurat_integrate)
export(SrtAppend)
export(SrtReorder)
export(Standard_SCP)
export(StatPlot)
export(Uncorrected_integrate)
export(VelocityPlot)
export(VolcanoPlot)
export(adata_to_srt)
export(adjcolors)
export(as_matrix)
export(blendcolors)
export(capitalize)
export(check_DataType)
export(check_Python)
export(check_R)
export(check_python_element)
export(check_srtList)
export(check_srtMerge)
export(compute_velocity_on_grid)
export(db_DoubletDetection)
export(db_Scrublet)
export(db_scDblFinder)
export(db_scds)
export(download)
export(drop_data)
export(exist_Python_pkgs)
export(fastMNN_integrate)
export(find_conda)
export(geom_alluvial)
export(geom_alluvial_label)
export(geom_alluvial_text)
export(geom_sankey)
export(geom_sankey_bump)
export(geom_sankey_label)
export(geom_sankey_text)
export(get_vars)
export(installed_Python_pkgs)
export(invoke)
export(isOutlier)
export(iterchunks)
export(make_long)
export(palette_scp)
export(panel_fix)
export(panel_fix_single)
export(scVI_integrate)
export(segementsDf)
export(show_palettes)
export(slim_data)
export(srt_to_adata)
export(theme_alluvial)
export(theme_blank)
export(theme_sankey)
export(theme_sankey_bump)
export(theme_scp)
export(tochunks)
export(try_get)
export(unnest)
importFrom(BiocParallel,"bpRNGseed<-")
importFrom(BiocParallel,"bpprogressbar<-")
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,bpaggregate)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpworkers)
importFrom(BiocParallel,ipcid)
importFrom(BiocParallel,ipclock)
importFrom(BiocParallel,ipcunlock)
importFrom(ComplexHeatmap,"%v%")
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,HeatmapAnnotation)
importFrom(ComplexHeatmap,Legend)
importFrom(ComplexHeatmap,anno_block)
importFrom(ComplexHeatmap,anno_customize)
importFrom(ComplexHeatmap,anno_empty)
importFrom(ComplexHeatmap,anno_mark)
importFrom(ComplexHeatmap,anno_simple)
importFrom(ComplexHeatmap,anno_textbox)
importFrom(ComplexHeatmap,cluster_within_group)
importFrom(ComplexHeatmap,decorate_annotation)
importFrom(ComplexHeatmap,decorate_heatmap_body)
importFrom(ComplexHeatmap,draw)
importFrom(ComplexHeatmap,height.HeatmapAnnotation)
importFrom(ComplexHeatmap,height.Legends)
importFrom(ComplexHeatmap,merge_dendrogram)
importFrom(ComplexHeatmap,pindex)
importFrom(ComplexHeatmap,restore_matrix)
importFrom(ComplexHeatmap,row_order)
importFrom(ComplexHeatmap,width.HeatmapAnnotation)
importFrom(ComplexHeatmap,width.Legends)
importFrom(Matrix,colMeans)
importFrom(Matrix,colSums)
importFrom(Matrix,rowMeans)
importFrom(Matrix,rowSums)
importFrom(Matrix,sparseMatrix)
importFrom(Matrix,t)
importFrom(R.cache,getCacheRootPath)
importFrom(R.cache,loadCache)
importFrom(R.cache,readCacheHeader)
importFrom(R.cache,saveCache)
importFrom(Seurat,"DefaultAssay<-")
importFrom(Seurat,"Idents<-")
importFrom(Seurat,"Key<-")
importFrom(Seurat,"Misc<-")
importFrom(Seurat,"Tool<-")
importFrom(Seurat,"VariableFeatures<-")
importFrom(Seurat,AddMetaData)
importFrom(Seurat,AddModuleScore)
importFrom(Seurat,Assays)
importFrom(Seurat,AverageExpression)
importFrom(Seurat,CaseMatch)
importFrom(Seurat,Cells)
importFrom(Seurat,CreateAssayObject)
importFrom(Seurat,CreateDimReducObject)
importFrom(Seurat,CreateSeuratObject)
importFrom(Seurat,DefaultAssay)
importFrom(Seurat,Embeddings)
importFrom(Seurat,FetchData)
importFrom(Seurat,FindClusters)
importFrom(Seurat,FindIntegrationAnchors)
importFrom(Seurat,FindMarkers)
importFrom(Seurat,FindNeighbors)
importFrom(Seurat,FindTransferAnchors)
importFrom(Seurat,FindVariableFeatures)
importFrom(Seurat,FoldChange)
importFrom(Seurat,GetAssay)
importFrom(Seurat,GetAssayData)
importFrom(Seurat,Idents)
importFrom(Seurat,IntegrateData)
importFrom(Seurat,IntegrateEmbeddings)
importFrom(Seurat,Key)
importFrom(Seurat,LogSeuratCommand)
importFrom(Seurat,Misc)
importFrom(Seurat,NormalizeData)
importFrom(Seurat,PercentageFeatureSet)
importFrom(Seurat,PrepSCTIntegration)
importFrom(Seurat,ProjectDim)
importFrom(Seurat,ProjectUMAP)
importFrom(Seurat,Reductions)
importFrom(Seurat,RunICA)
importFrom(Seurat,RunPCA)
importFrom(Seurat,RunTSNE)
importFrom(Seurat,SCTResults)
importFrom(Seurat,SCTransform)
importFrom(Seurat,ScaleData)
importFrom(Seurat,SelectIntegrationFeatures)
importFrom(Seurat,SetAssayData)
importFrom(Seurat,SplitObject)
importFrom(Seurat,TransferData)
importFrom(Seurat,UpdateSymbolList)
importFrom(Seurat,VariableFeatures)
importFrom(Seurat,WhichCells)
importFrom(Seurat,as.Graph)
importFrom(Seurat,as.SingleCellExperiment)
importFrom(Seurat,as.sparse)
importFrom(SeuratObject,CheckGC)
importFrom(SeuratObject,DefaultAssay)
importFrom(SeuratObject,Distances)
importFrom(SeuratObject,Embeddings)
importFrom(SeuratObject,FetchData)
importFrom(SeuratObject,GetAssayData)
importFrom(SeuratObject,Idents)
importFrom(SeuratObject,Indices)
importFrom(SeuratObject,Loadings)
importFrom(SeuratObject,PackageCheck)
importFrom(SeuratObject,SetIdent)
importFrom(SeuratObject,Stdev)
importFrom(SeuratObject,WhichCells)
importFrom(SeuratObject,as.Graph)
importFrom(SeuratObject,as.sparse)
importFrom(Signac,RunSVD)
importFrom(Signac,RunTFIDF)
importFrom(biomaRt,getBM)
importFrom(biomaRt,listAttributes)
importFrom(biomaRt,listDatasets)
importFrom(biomaRt,listEnsemblArchives)
importFrom(biomaRt,useDataset)
importFrom(biomaRt,useEnsembl)
importFrom(biomaRt,useMart)
importFrom(circlize,chordDiagram)
importFrom(circlize,circos.clear)
importFrom(circlize,colorRamp2)
importFrom(clusterProfiler,GSEA)
importFrom(clusterProfiler,enricher)
importFrom(clusterProfiler,simplify)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(dplyr,"%>%")
importFrom(dplyr,.data)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,arrange_at)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,desc)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_at)
importFrom(dplyr,mutate)
importFrom(dplyr,n)
importFrom(dplyr,pull)
importFrom(dplyr,reframe)
importFrom(dplyr,slice_head)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_at)
importFrom(ggforce,geom_mark_ellipse)
importFrom(ggforce,geom_mark_hull)
importFrom(ggnewscale,new_scale)
importFrom(ggnewscale,new_scale_color)
importFrom(ggnewscale,new_scale_fill)
importFrom(ggplot2,"%+replace%")
importFrom(ggplot2,.pt)
importFrom(ggplot2,aes)
importFrom(ggplot2,after_stat)
importFrom(ggplot2,alpha)
importFrom(ggplot2,annotate)
importFrom(ggplot2,annotation_custom)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,coord_polar)
importFrom(ggplot2,draw_key_point)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_null)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_blank)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_col)
importFrom(ggplot2,geom_count)
importFrom(ggplot2,geom_curve)
importFrom(ggplot2,geom_density_2d)
importFrom(ggplot2,geom_hex)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_label)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_linerange)
importFrom(ggplot2,geom_path)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_rug)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_sf)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_colorbar)
importFrom(ggplot2,guide_colourbar)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guide_none)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer_data)
importFrom(ggplot2,layer_scales)
importFrom(ggplot2,margin)
importFrom(ggplot2,mean_sdl)
importFrom(ggplot2,panel_cols)
importFrom(ggplot2,panel_rows)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_dodge2)
importFrom(ggplot2,position_identity)
importFrom(ggplot2,position_jitter)
importFrom(ggplot2,position_jitterdodge)
importFrom(ggplot2,position_stack)
importFrom(ggplot2,scale_alpha)
importFrom(ggplot2,scale_alpha_continuous)
importFrom(ggplot2,scale_alpha_discrete)
importFrom(ggplot2,scale_alpha_identity)
importFrom(ggplot2,scale_alpha_manual)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_identity)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_gradient)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_gradientn)
importFrom(ggplot2,scale_fill_identity)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linewidth)
importFrom(ggplot2,scale_linewidth_continuous)
importFrom(ggplot2,scale_shape_identity)
importFrom(ggplot2,scale_size)
importFrom(ggplot2,scale_size_area)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_size_discrete)
importFrom(ggplot2,scale_size_identity)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_discrete)
importFrom(ggplot2,stat_density2d)
importFrom(ggplot2,stat_density_2d)
importFrom(ggplot2,stat_summary)
importFrom(ggplot2,stat_summary_hex)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,wrap_dims)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggplot2,zeroGrob)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,col2rgb)
importFrom(grDevices,colorRamp)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,rgb)
importFrom(graphics,par)
importFrom(graphics,rect)
importFrom(graphics,text)
importFrom(grid,addGrob)
importFrom(grid,arrow)
importFrom(grid,convertHeight)
importFrom(grid,convertUnit)
importFrom(grid,convertWidth)
importFrom(grid,gList)
importFrom(grid,gpar)
importFrom(grid,grid.draw)
importFrom(grid,grid.grabExpr)
importFrom(grid,grid.lines)
importFrom(grid,grid.points)
importFrom(grid,grid.rect)
importFrom(grid,grid.text)
importFrom(grid,grob)
importFrom(grid,grobHeight)
importFrom(grid,grobTree)
importFrom(grid,grobWidth)
importFrom(grid,is.grob)
importFrom(grid,is.unit)
importFrom(grid,linesGrob)
importFrom(grid,rasterGrob)
importFrom(grid,textGrob)
importFrom(grid,unit)
importFrom(grid,unit.pmax)
importFrom(grid,unitType)
importFrom(grid,viewport)
importFrom(gridGraphics,echoGrob)
importFrom(gtable,gtable)
importFrom(gtable,gtable_add_cols)
importFrom(gtable,gtable_add_grob)
importFrom(gtable,gtable_add_padding)
importFrom(gtable,gtable_add_rows)
importFrom(gtable,gtable_col)
importFrom(gtable,is.gtable)
importFrom(igraph,V)
importFrom(igraph,as_adjacency_matrix)
importFrom(igraph,as_data_frame)
importFrom(igraph,cluster_fast_greedy)
importFrom(igraph,cluster_fluid_communities)
importFrom(igraph,cluster_infomap)
importFrom(igraph,cluster_leiden)
importFrom(igraph,cluster_louvain)
importFrom(igraph,cluster_spinglass)
importFrom(igraph,cluster_walktrap)
importFrom(igraph,degree)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,layout_as_tree)
importFrom(igraph,layout_in_circle)
importFrom(igraph,layout_on_grid)
importFrom(igraph,layout_with_dh)
importFrom(igraph,layout_with_drl)
importFrom(igraph,layout_with_fr)
importFrom(igraph,layout_with_gem)
importFrom(igraph,layout_with_graphopt)
importFrom(igraph,layout_with_kk)
importFrom(igraph,layout_with_lgl)
importFrom(igraph,layout_with_mds)
importFrom(igraph,neighbors)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,getFunction)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,slotNames)
importFrom(parallelDist,parDist)
importFrom(patchwork,wrap_plots)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(reticulate,import)
importFrom(reticulate,iterate)
importFrom(reticulate,np_array)
importFrom(reticulate,py_to_r)
importFrom(rlang,"%||%")
importFrom(rlang,call2)
importFrom(rlang,caller_env)
importFrom(rlang,env)
importFrom(rlang,env_bind)
importFrom(rlang,env_get)
importFrom(rlang,is_character)
importFrom(rlang,is_function)
importFrom(rlang,is_null)
importFrom(rlang,is_scalar_character)
importFrom(rlang,set_names)
importFrom(rlang,syms)
importFrom(slingshot,slingBranchID)
importFrom(slingshot,slingPseudotime)
importFrom(slingshot,slingshot)
importFrom(stats,aggregate)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,binom.test)
importFrom(stats,cmdscale)
importFrom(stats,dist)
importFrom(stats,formula)
importFrom(stats,hclust)
importFrom(stats,kmeans)
importFrom(stats,loess)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,order.dendrogram)
importFrom(stats,p.adjust)
importFrom(stats,pbeta)
importFrom(stats,pnorm)
importFrom(stats,predict)
importFrom(stats,quantile)
importFrom(stats,reorder)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(stats,xtabs)
importFrom(utils,askYesNo)
importFrom(utils,capture.output)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,modifyList)
importFrom(utils,packageVersion)
importFrom(utils,read.table)
importFrom(utils,select.list)
useDynLib(SCP)