# Generated by roxygen2: do not edit by hand

export(add.set.column)
export(add_metadata)
export(alluvialServer)
export(alluvialUI)
export(check_user_access)
export(cnetPlotServer)
export(cnetPlotUI)
export(create_access_yaml)
export(dendrogramServer)
export(dendrogramUI)
export(distillPlotServer)
export(distillPlotUI)
export(downloadButtonServer)
export(downloadButtonUI)
export(enrichServer)
export(enrichUI)
export(enrich_to_genetonic)
export(enrichmapServer)
export(enrichmapUI)
export(format_genes)
export(fromList.with.names)
export(fuzzyPlotServer)
export(fuzzyPlotUI)
export(genePlotServer)
export(genePlotUI)
export(get_access_path)
export(get_config)
export(get_config_path)
export(get_degplot)
export(get_gene_counts)
export(get_project_name_from_path)
export(get_upset_table)
export(get_y_init)
export(getcountplot)
export(gs_radar)
export(heatmapServer)
export(heatmapUI)
export(helpButtonServer)
export(helpButtonUI)
export(horizonServer)
export(horizonUI)
export(in_admin_group)
export(init_local_config)
export(install_carnation)
export(is_site_admin)
export(is_valid_pattern_obj)
export(loadDataServer)
export(loadDataUI)
export(maPlotServer)
export(maPlotUI)
export(makeEnrichResult)
export(make_example_carnation_object)
export(make_final_object)
export(materialize_carnation_object)
export(metadataServer)
export(metadataUI)
export(my.summary)
export(patternPlotServer)
export(patternPlotUI)
export(pcaPlotServer)
export(pcaPlotUI)
export(plotMA.label)
export(plotMA.label_ly)
export(plotPCA.ly)
export(plotPCA.san)
export(plotScatter.label)
export(plotScatter.label_ly)
export(radarServer)
export(radarUI)
export(read_access_yaml)
export(run_carnation)
export(saveServer)
export(saveUI)
export(save_access_yaml)
export(scatterPlotServer)
export(scatterPlotUI)
export(set_config)
export(settingsServer)
export(settingsUI)
export(summarize_res_list)
export(sumovPlotServer)
export(sumovPlotUI)
export(top.genes)
export(upsetPlotServer)
export(upsetPlotUI)
export(validate_carnation_object)
import(ggplot2)
import(shiny, except = c(dataTableOutput, renderDataTable))
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,bplapply)
importFrom(ComplexUpset,intersection_size)
importFrom(ComplexUpset,upset)
importFrom(ComplexUpset,upset_modify_themes)
importFrom(ComplexUpset,upset_query)
importFrom(DESeq2,DESeq)
importFrom(DESeq2,DESeqDataSetFromMatrix)
importFrom(DESeq2,counts)
importFrom(DESeq2,design)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,makeExampleDESeqDataSet)
importFrom(DESeq2,normalizationFactors)
importFrom(DESeq2,plotPCA)
importFrom(DESeq2,results)
importFrom(DESeq2,sizeFactors)
importFrom(DESeq2,varianceStabilizingTransformation)
importFrom(DT,DTOutput)
importFrom(DT,dataTableProxy)
importFrom(DT,datatable)
importFrom(DT,formatSignif)
importFrom(DT,formatStyle)
importFrom(DT,renderDT)
importFrom(DT,selectCells)
importFrom(DT,selectPage)
importFrom(DT,selectRows)
importFrom(GeneTonic,cluster_markov)
importFrom(GeneTonic,distill_enrichment)
importFrom(GeneTonic,enrichment_map)
importFrom(GeneTonic,get_aggrscores)
importFrom(GeneTonic,gs_alluvial)
importFrom(GeneTonic,gs_dendro)
importFrom(GeneTonic,gs_fuzzyclustering)
importFrom(GeneTonic,gs_horizon)
importFrom(GeneTonic,gs_summary_overview)
importFrom(GeneTonic,gs_summary_overview_pair)
importFrom(GeneTonic,shake_enrichResult)
importFrom(GeneTonic,shake_gsenrichResult)
importFrom(MatrixGenerics,rowVars)
importFrom(RColorBrewer,brewer.pal)
importFrom(SummarizedExperiment,"colData<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,colData)
importFrom(colorspace,qualitative_hcl)
importFrom(colorspace,rainbow_hcl)
importFrom(dendextend,as.ggdend)
importFrom(dendextend,get_branches_heights)
importFrom(dplyr,"%>%")
importFrom(dplyr,all_of)
importFrom(dplyr,any_of)
importFrom(dplyr,arrange)
importFrom(dplyr,case_when)
importFrom(dplyr,everything)
importFrom(dplyr,filter)
importFrom(dplyr,inner_join)
importFrom(dplyr,mutate)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(enrichplot,cnetplot)
importFrom(ggrepel,geom_label_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,par)
importFrom(heatmaply,heatmaply)
importFrom(heatmaply,is.plotly)
importFrom(htmltools,tagAppendChild)
importFrom(htmltools,tagAppendChildren)
importFrom(htmltools,tagList)
importFrom(htmltools,tags)
importFrom(htmltools,withTags)
importFrom(igraph,"V<-")
importFrom(igraph,V)
importFrom(methods,.hasSlot)
importFrom(methods,new)
importFrom(plotly,add_markers)
importFrom(plotly,add_trace)
importFrom(plotly,event_data)
importFrom(plotly,event_register)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,plotlyProxy)
importFrom(plotly,renderPlotly)
importFrom(plotly,save_image)
importFrom(plotly,toWebGL)
importFrom(reticulate,py_install)
importFrom(reticulate,use_virtualenv)
importFrom(rintrojs,introBox)
importFrom(rintrojs,introjs)
importFrom(rintrojs,introjsUI)
importFrom(scales,alpha)
importFrom(shinyBS,bsCollapse)
importFrom(shinyBS,bsCollapsePanel)
importFrom(shinyBS,updateCollapse)
importFrom(shinyWidgets,dropdownButton)
importFrom(shinyWidgets,tooltipOptions)
importFrom(shinycssloaders,withSpinner)
importFrom(shinymanager,check_credentials)
importFrom(shinymanager,create_db)
importFrom(shinymanager,secure_app)
importFrom(shinymanager,secure_server)
importFrom(shinythemes,shinytheme)
importFrom(sortable,add_rank_list)
importFrom(sortable,bucket_list)
importFrom(stats,as.formula)
importFrom(stats,median)
importFrom(stats,prcomp)
importFrom(stats,setNames)
importFrom(tools,file_path_sans_ext)
importFrom(utils,capture.output)
importFrom(utils,packageName)
importFrom(utils,read.table)
importFrom(utils,str)
importFrom(viridisLite,viridis)
importFrom(visNetwork,renderVisNetwork)
importFrom(visNetwork,visIgraph)
importFrom(visNetwork,visNetworkOutput)
importFrom(visNetwork,visNodes)
importFrom(visNetwork,visOptions)
importFrom(yaml,read_yaml)
importFrom(yaml,write_yaml)
