# Generated by roxygen2: do not edit by hand

S3method("[",expressionDrugSensitivityAssociation)
S3method("[",perturbationChanges)
S3method(as.table,referenceComparison)
S3method(dim,expressionDrugSensitivityAssociation)
S3method(dim,perturbationChanges)
S3method(dimnames,expressionDrugSensitivityAssociation)
S3method(dimnames,perturbationChanges)
S3method(plot,perturbationChanges)
S3method(plot,referenceComparison)
S3method(print,similarPerturbations)
export(analyseDrugSetEnrichment)
export(cTRAP)
export(convertENSEMBLtoGeneSymbols)
export(convertGeneIdentifiers)
export(downloadENCODEknockdownMetadata)
export(filterCMapMetadata)
export(getCMapConditions)
export(getCMapPerturbationTypes)
export(launchCMapDataLoader)
export(launchDiffExprLoader)
export(launchDrugSetEnrichmentAnalyser)
export(launchMetadataViewer)
export(launchResultPlotter)
export(listExpressionDrugSensitivityAssociation)
export(loadCMapData)
export(loadCMapZscores)
export(loadDrugDescriptors)
export(loadENCODEsamples)
export(loadExpressionDrugSensitivityAssociation)
export(parseCMapID)
export(performDifferentialExpression)
export(plotDrugSetEnrichment)
export(plotTargetingDrugsVSsimilarPerturbations)
export(predictTargetingDrugs)
export(prepareCMapPerturbations)
export(prepareDrugSets)
export(prepareENCODEgeneExpression)
export(rankSimilarPerturbations)
importFrom(AnnotationDbi,select)
importFrom(AnnotationHub,AnnotationHub)
importFrom(AnnotationHub,query)
importFrom(DT,DTOutput)
importFrom(DT,dataTableProxy)
importFrom(DT,datatable)
importFrom(DT,formatSignif)
importFrom(DT,renderDT)
importFrom(DT,replaceData)
importFrom(R.utils,capitalize)
importFrom(R.utils,gunzip)
importFrom(R.utils,isGzipped)
importFrom(R.utils,renameFile)
importFrom(binr,bins)
importFrom(binr,bins.getvals)
importFrom(cowplot,draw_label)
importFrom(cowplot,ggdraw)
importFrom(cowplot,plot_grid)
importFrom(data.table,":=")
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,rbindlist)
importFrom(data.table,setkeyv)
importFrom(data.table,transpose)
importFrom(dplyr,bind_rows)
importFrom(fastmatch,fmatch)
importFrom(fgsea,calcGseaStat)
importFrom(fgsea,fgsea)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,expansion)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,geom_density_2d)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_raster)
importFrom(ggplot2,geom_rug)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,scale_y_reverse)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(graphics,plot)
importFrom(highcharter,"%>%")
importFrom(highcharter,JS)
importFrom(highcharter,hc_title)
importFrom(highcharter,hc_tooltip)
importFrom(highcharter,hcaes)
importFrom(highcharter,hchart)
importFrom(highcharter,highchart)
importFrom(highcharter,highchartOutput)
importFrom(highcharter,renderHighchart)
importFrom(htmltools,tagQuery)
importFrom(httr,GET)
importFrom(httr,POST)
importFrom(httr,content)
importFrom(httr,status_code)
importFrom(httr,stop_for_status)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(methods,is)
importFrom(methods,new)
importFrom(parallel,mclapply)
importFrom(pbapply,closepb)
importFrom(pbapply,getpb)
importFrom(pbapply,pblapply)
importFrom(pbapply,setpb)
importFrom(pbapply,startpb)
importFrom(purrr,"pluck<-")
importFrom(purrr,pluck)
importFrom(qs2,qs_read)
importFrom(qs2,qs_save)
importFrom(readxl,read_excel)
importFrom(reshape2,dcast)
importFrom(rhdf5,h5closeAll)
importFrom(rhdf5,h5createDataset)
importFrom(rhdf5,h5createFile)
importFrom(rhdf5,h5ls)
importFrom(rhdf5,h5read)
importFrom(rhdf5,h5readAttributes)
importFrom(rhdf5,h5write)
importFrom(rlang,"!!!")
importFrom(scales,extended_breaks)
importFrom(shiny,HTML)
importFrom(shiny,NS)
importFrom(shiny,actionButton)
importFrom(shiny,actionLink)
importFrom(shiny,brushedPoints)
importFrom(shiny,checkboxGroupInput)
importFrom(shiny,checkboxInput)
importFrom(shiny,column)
importFrom(shiny,conditionalPanel)
importFrom(shiny,div)
importFrom(shiny,downloadHandler)
importFrom(shiny,downloadLink)
importFrom(shiny,eventReactive)
importFrom(shiny,fileInput)
importFrom(shiny,fluidRow)
importFrom(shiny,h3)
importFrom(shiny,helpText)
importFrom(shiny,hr)
importFrom(shiny,icon)
importFrom(shiny,incProgress)
importFrom(shiny,includeCSS)
importFrom(shiny,includeScript)
importFrom(shiny,is.reactive)
importFrom(shiny,isolate)
importFrom(shiny,mainPanel)
importFrom(shiny,modalButton)
importFrom(shiny,modalDialog)
importFrom(shiny,moduleServer)
importFrom(shiny,navbarMenu)
importFrom(shiny,navbarPage)
importFrom(shiny,numericInput)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,plotOutput)
importFrom(shiny,reactive)
importFrom(shiny,reactivePoll)
importFrom(shiny,reactiveVal)
importFrom(shiny,reactiveValues)
importFrom(shiny,removeModal)
importFrom(shiny,renderPlot)
importFrom(shiny,renderText)
importFrom(shiny,renderUI)
importFrom(shiny,req)
importFrom(shiny,runApp)
importFrom(shiny,selectizeInput)
importFrom(shiny,shinyApp)
importFrom(shiny,showModal)
importFrom(shiny,showNotification)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,span)
importFrom(shiny,stopApp)
importFrom(shiny,tabPanel)
importFrom(shiny,tabsetPanel)
importFrom(shiny,tagAppendAttributes)
importFrom(shiny,tagAppendChildren)
importFrom(shiny,tagList)
importFrom(shiny,tags)
importFrom(shiny,textAreaInput)
importFrom(shiny,textInput)
importFrom(shiny,textOutput)
importFrom(shiny,uiOutput)
importFrom(shiny,updateSelectizeInput)
importFrom(shiny,updateTextInput)
importFrom(shiny,withProgress)
importFrom(shinycssloaders,withSpinner)
importFrom(stats,aggregate)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,model.matrix)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(tibble,tibble)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(utils,askYesNo)
importFrom(utils,assignInNamespace)
importFrom(utils,download.file)
importFrom(utils,getFromNamespace)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,tail)
importFrom(utils,unzip)
