# Generated by roxygen2: do not edit by hand

export(adj_mod)
export(aggr_rep)
export(auc_bar)
export(auc_stat)
export(auc_violin)
export(cluster_cell)
export(coclus_opt)
export(coclus_roc)
export(cocluster)
export(com_factor)
export(custom_shiny)
export(deg_ovl)
export(desired_bulk_shiny)
export(edit_tar)
export(filter_cell)
export(filter_data)
export(filter_iter)
export(matrix_hm)
export(mean_auc_bar)
export(network)
export(norm_data)
export(norm_multi)
export(plot_dim)
export(profile_gene)
export(random_para)
export(read_cache)
export(read_fr)
export(read_hdf5)
export(reduce_rep)
export(refine_cluster)
export(return_feature)
export(save_cache)
export(shiny_shm)
export(spatial_enrich)
export(spatial_hm)
export(spd_auc_violin)
export(sub_asg)
export(sub_data)
export(submatrix)
export(true_bulk)
export(update_feature)
export(write_hdf5)
importFrom(BiocFileCache,BiocFileCache)
importFrom(BiocFileCache,bfccache)
importFrom(BiocFileCache,bfcinfo)
importFrom(BiocFileCache,bfcnew)
importFrom(BiocFileCache,bfcquery)
importFrom(BiocFileCache,bfcremove)
importFrom(BiocFileCache,bfcrpath)
importFrom(BiocParallel,"bpRNGseed<-")
importFrom(BiocParallel,"bpworkers<-")
importFrom(BiocParallel,BatchtoolsParam)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bpRNGseed)
importFrom(BiocParallel,bplapply)
importFrom(BiocParallel,bpnworkers)
importFrom(BiocParallel,bpworkers)
importFrom(BiocParallel,register)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,results)
importFrom(DESeq2,rlog)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(HDF5Array,loadHDF5SummarizedExperiment)
importFrom(HDF5Array,saveHDF5SummarizedExperiment)
importFrom(Matrix,Matrix)
importFrom(Matrix,colSums)
importFrom(Matrix,rowSums)
importFrom(S4Vectors,DataFrame)
importFrom(SingleCellExperiment,"colLabels<-")
importFrom(SingleCellExperiment,"logcounts<-")
importFrom(SingleCellExperiment,SingleCellExperiment)
importFrom(SingleCellExperiment,cbind)
importFrom(SingleCellExperiment,colLabels)
importFrom(SingleCellExperiment,logcounts)
importFrom(SingleCellExperiment,reducedDim)
importFrom(SingleCellExperiment,reducedDimNames)
importFrom(SummarizedExperiment,"assay<-")
importFrom(SummarizedExperiment,"assayNames<-")
importFrom(SummarizedExperiment,"assays<-")
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,"rowData<-")
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(SummarizedExperiment,rowData)
importFrom(UpSetR,fromList)
importFrom(UpSetR,upset)
importFrom(WGCNA,TOMsimilarity)
importFrom(WGCNA,adjacency)
importFrom(av,av_capture_graphics)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(data.table,setDF)
importFrom(distinct,distinct_test)
importFrom(distinct,log2_FC)
importFrom(dynamicTreeCut,cutreeHybrid)
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,estimateDisp)
importFrom(edgeR,glmFit)
importFrom(edgeR,glmLRT)
importFrom(edgeR,topTags)
importFrom(flashClust,flashClust)
importFrom(genefilter,cv)
importFrom(genefilter,filterfun)
importFrom(genefilter,genefilter)
importFrom(genefilter,pOverA)
importFrom(ggdendro,dendro_data)
importFrom(ggplot2,aes)
importFrom(ggplot2,alpha)
importFrom(ggplot2,annotation_raster)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplotGrob)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer_data)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,position_dodge2)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggplotify,as.ggplot)
importFrom(gplots,col2hex)
importFrom(gplots,heatmap.2)
importFrom(gplots,venn)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(grDevices,dev.off)
importFrom(grDevices,png)
importFrom(grImport,PostScriptTrace)
importFrom(graphics,image)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,title)
importFrom(grid,grobTree)
importFrom(grid,unit)
importFrom(gridExtra,arrangeGrob)
importFrom(gridExtra,grid.arrange)
importFrom(htmlwidgets,saveWidget)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,as_data_frame)
importFrom(igraph,cluster_edge_betweenness)
importFrom(igraph,cluster_fast_greedy)
importFrom(igraph,cluster_leading_eigen)
importFrom(igraph,cluster_spinglass)
importFrom(igraph,cluster_walktrap)
importFrom(igraph,delete_edges)
importFrom(igraph,delete_vertices)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,layout_in_circle)
importFrom(igraph,layout_with_fr)
importFrom(limma,contrasts.fit)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,makeContrasts)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(magick,image_charcoal)
importFrom(magick,image_read)
importFrom(methods,as)
importFrom(methods,is)
importFrom(pROC,auc)
importFrom(pROC,coords)
importFrom(pROC,roc)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(plotly,"%>%")
importFrom(plotly,as_widget)
importFrom(plotly,gg2list)
importFrom(plotly,layout)
importFrom(plotly,subplot)
importFrom(rappdirs,user_cache_dir)
importFrom(reshape2,melt)
importFrom(rols,term)
importFrom(rols,termDesc)
importFrom(rsvg,rsvg_ps)
importFrom(scater,plotColData)
importFrom(scater,runTSNE)
importFrom(scater,runUMAP)
importFrom(scran,buildKNNGraph)
importFrom(scran,buildSNNGraph)
importFrom(scran,computeSumFactors)
importFrom(scran,denoisePCA)
importFrom(scran,getTopHVGs)
importFrom(scran,modelGeneVar)
importFrom(scran,quickCluster)
importFrom(scuttle,calculateCPM)
importFrom(scuttle,logNormCounts)
importFrom(shiny,HTML)
importFrom(shiny,actionButton)
importFrom(shiny,div)
importFrom(shiny,fluidRow)
importFrom(shiny,htmlOutput)
importFrom(shiny,icon)
importFrom(shiny,incProgress)
importFrom(shiny,modalButton)
importFrom(shiny,modalDialog)
importFrom(shiny,need)
importFrom(shiny,numericInput)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,plotOutput)
importFrom(shiny,radioButtons)
importFrom(shiny,reactive)
importFrom(shiny,reactiveValues)
importFrom(shiny,renderPlot)
importFrom(shiny,renderUI)
importFrom(shiny,runApp)
importFrom(shiny,selectInput)
importFrom(shiny,shinyApp)
importFrom(shiny,shinyServer)
importFrom(shiny,shinyUI)
importFrom(shiny,showModal)
importFrom(shiny,span)
importFrom(shiny,splitLayout)
importFrom(shiny,tagList)
importFrom(shiny,tags)
importFrom(shiny,textInput)
importFrom(shiny,updateRadioButtons)
importFrom(shiny,updateSelectInput)
importFrom(shiny,validate)
importFrom(shiny,withProgress)
importFrom(shinydashboard,box)
importFrom(shinydashboard,dashboardBody)
importFrom(shinydashboard,dashboardHeader)
importFrom(shinydashboard,dashboardPage)
importFrom(shinydashboard,dashboardSidebar)
importFrom(shinydashboard,menuItem)
importFrom(shinydashboard,menuSubItem)
importFrom(shinydashboard,sidebarMenu)
importFrom(shinydashboard,tabItem)
importFrom(shinydashboard,tabItems)
importFrom(stats,as.dendrogram)
importFrom(stats,as.dist)
importFrom(stats,cor)
importFrom(stats,dist)
importFrom(stats,hclust)
importFrom(stats,model.matrix)
importFrom(stats,order.dendrogram)
importFrom(stats,quantile)
importFrom(stats,sd)
importFrom(utils,combn)
importFrom(utils,head)
importFrom(utils,tar)
importFrom(utils,untar)
importFrom(utils,unzip)
importFrom(utils,write.table)
importFrom(visNetwork,renderVisNetwork)
importFrom(visNetwork,visIgraphLayout)
importFrom(visNetwork,visNetwork)
importFrom(visNetwork,visNetworkOutput)
importFrom(visNetwork,visOptions)
importFrom(xml2,read_xml)
importFrom(xml2,write_xml)
importFrom(xml2,xml_add_child)
importFrom(xml2,xml_add_sibling)
importFrom(xml2,xml_attr)
importFrom(xml2,xml_attrs)
importFrom(xml2,xml_children)
importFrom(xml2,xml_length)
importFrom(xml2,xml_name)
importFrom(xml2,xml_new_root)
importFrom(xml2,xml_remove)
importFrom(xml2,xml_set_attr)
importFrom(xml2,xml_set_text)
importFrom(xml2,xml_text)
importFrom(yaml,write_yaml)
importFrom(yaml,yaml.load_file)
