# Generated by roxygen2: do not edit by hand

S3method("[",GEandAScorrelation)
S3method("[",sticky)
S3method(as.table,GEandAScorrelation)
S3method(plot,GEandAScorrelation)
S3method(print,GEandAScorrelation)
S3method(print,geneList)
S3method(print,splicingEventPlot)
S3method(print,splicingEventPlotList)
S3method(survfit,survTerms)
S3method(t,sticky)
export(assignValuePerPatient)
export(assignValuePerSubject)
export(calculateLoadingsContribution)
export(convertGeneIdentifiers)
export(correlateGEandAS)
export(createGroupByAttribute)
export(diffAnalyses)
export(discardLowCoveragePSIvalues)
export(ensemblToUniprot)
export(filterGeneExpr)
export(filterGroups)
export(filterPSI)
export(getAttributesTime)
export(getDownloadsFolder)
export(getFirebrowseCohorts)
export(getFirebrowseDataTypes)
export(getFirebrowseDates)
export(getGeneList)
export(getGenesFromSplicingEvents)
export(getGtexDataTypes)
export(getGtexReleases)
export(getGtexTissues)
export(getMatchingSamples)
export(getPatientFromSample)
export(getSampleFromPatient)
export(getSampleFromSubject)
export(getSplicingEventData)
export(getSplicingEventFromGenes)
export(getSplicingEventTypes)
export(getSubjectFromSample)
export(getTCGAcohorts)
export(getTCGAdataTypes)
export(getTCGAdates)
export(getValuePerPatient)
export(getValuePerSubject)
export(groupPerElem)
export(isFirebrowseUp)
export(labelBasedOnCutoff)
export(listSplicingAnnotations)
export(loadAnnotation)
export(loadFirebrowseData)
export(loadGtexData)
export(loadLocalFiles)
export(loadSRAproject)
export(loadTCGAdata)
export(normaliseGeneExpression)
export(normalizeGeneExpression)
export(optimalSurvivalCutoff)
export(parseCategoricalGroups)
export(parseMatsAnnotation)
export(parseMisoAnnotation)
export(parseSampleGroups)
export(parseSplicingEvent)
export(parseSuppaAnnotation)
export(parseTCGAsampleInfo)
export(parseTCGAsampleTypes)
export(parseTcgaSampleInfo)
export(parseVastToolsAnnotation)
export(performICA)
export(performPCA)
export(plotCorrelation)
export(plotDistribution)
export(plotGeneExprPerSample)
export(plotGroupIndependence)
export(plotICA)
export(plotLibrarySize)
export(plotPCA)
export(plotPCAvariance)
export(plotProtein)
export(plotRowStats)
export(plotSplicingEvent)
export(plotSurvivalCurves)
export(plotSurvivalPvaluesByCutoff)
export(plotTranscripts)
export(plotVariance)
export(prepareAnnotationFromEvents)
export(prepareGeneQuant)
export(prepareJunctionQuant)
export(prepareSRAmetadata)
export(processSurvTerms)
export(psichomics)
export(quantifySplicing)
export(queryEnsemblByEvent)
export(queryEnsemblByGene)
export(readFile)
export(survdiffTerms)
export(testGroupIndependence)
export(testSurvival)
exportMethods(colSums)
importFrom(AnnotationDbi,select)
importFrom(AnnotationHub,AnnotationHub)
importFrom(AnnotationHub,getAnnotationHubOption)
importFrom(AnnotationHub,mcols)
importFrom(AnnotationHub,query)
importFrom(AnnotationHub,setAnnotationHubOption)
importFrom(BiocFileCache,BiocFileCache)
importFrom(DT,JS)
importFrom(DT,dataTableOutput)
importFrom(DT,dataTableProxy)
importFrom(DT,renderDataTable)
importFrom(DT,replaceData)
importFrom(DT,selectRows)
importFrom(R.utils,capitalize)
importFrom(R.utils,decapitalize)
importFrom(R.utils,decompressFile)
importFrom(R.utils,gunzip)
importFrom(R.utils,withTimeout)
importFrom(Rcpp,sourceCpp)
importFrom(Rfast,colMedians)
importFrom(Rfast,rowMaxs)
importFrom(Rfast,rowMedians)
importFrom(Rfast,rowMins)
importFrom(Rfast,rowVars)
importFrom(Rfast,rowmeans)
importFrom(Rfast,rowrange)
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,end)
importFrom(SummarizedExperiment,seqnames)
importFrom(SummarizedExperiment,start)
importFrom(SummarizedExperiment,strand)
importFrom(XML,xmlAttrs)
importFrom(XML,xmlChildren)
importFrom(XML,xmlName)
importFrom(XML,xmlParse)
importFrom(XML,xmlRoot)
importFrom(XML,xmlToDataFrame)
importFrom(XML,xmlToList)
importFrom(XML,xmlTreeParse)
importFrom(cluster,clara)
importFrom(cluster,pam)
importFrom(cluster,silhouette)
importFrom(colourpicker,colourInput)
importFrom(colourpicker,updateColourInput)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,fwrite)
importFrom(data.table,setkeyv)
importFrom(data.table,setnames)
importFrom(data.table,setorderv)
importFrom(digest,digest)
importFrom(edgeR,"[.DGEList")
importFrom(edgeR,DGEList)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,cpm)
importFrom(edgeR,filterByExpr)
importFrom(fastICA,fastICA)
importFrom(fastmatch,"%fin%")
importFrom(fastmatch,fmatch)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_equal)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_density_2d)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_gradient2)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_light)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlim)
importFrom(ggplot2,ylim)
importFrom(ggrepel,geom_label_repel)
importFrom(grDevices,chull)
importFrom(graphics,plot)
importFrom(highcharter,"%>%")
importFrom(highcharter,JS)
importFrom(highcharter,data_to_boxplot)
importFrom(highcharter,fa_icon_mark)
importFrom(highcharter,hc_add_series)
importFrom(highcharter,hc_add_series_list)
importFrom(highcharter,hc_chart)
importFrom(highcharter,hc_credits)
importFrom(highcharter,hc_exporting)
importFrom(highcharter,hc_legend)
importFrom(highcharter,hc_plotOptions)
importFrom(highcharter,hc_series)
importFrom(highcharter,hc_subtitle)
importFrom(highcharter,hc_title)
importFrom(highcharter,hc_tooltip)
importFrom(highcharter,hc_xAxis)
importFrom(highcharter,hc_yAxis)
importFrom(highcharter,hchart)
importFrom(highcharter,highchart)
importFrom(highcharter,highchartOutput)
importFrom(highcharter,list_parse)
importFrom(highcharter,renderHighchart)
importFrom(highcharter,tooltip_table)
importFrom(htmltools,"htmlDependencies<-")
importFrom(htmltools,browsable)
importFrom(htmltools,htmlDependencies)
importFrom(htmltools,htmlDependency)
importFrom(htmltools,knit_print.html)
importFrom(htmltools,tagQuery)
importFrom(httr,GET)
importFrom(httr,content)
importFrom(httr,http_error)
importFrom(httr,stop_for_status)
importFrom(httr,timeout)
importFrom(httr,warn_for_status)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(limma,eBayes)
importFrom(limma,lmFit)
importFrom(limma,topTable)
importFrom(limma,voom)
importFrom(methods,is)
importFrom(pairsD3,pairsD3)
importFrom(pairsD3,pairsD3Output)
importFrom(pairsD3,renderPairsD3)
importFrom(plyr,dlply)
importFrom(plyr,ldply)
importFrom(plyr,rbind.fill)
importFrom(purrr,"pluck<-")
importFrom(purrr,pluck)
importFrom(recount,download_study)
importFrom(reshape2,melt)
importFrom(shiny,HTML)
importFrom(shiny,NS)
importFrom(shiny,Progress)
importFrom(shiny,a)
importFrom(shiny,actionButton)
importFrom(shiny,actionLink)
importFrom(shiny,addResourcePath)
importFrom(shiny,br)
importFrom(shiny,brushOpts)
importFrom(shiny,callModule)
importFrom(shiny,checkboxGroupInput)
importFrom(shiny,checkboxInput)
importFrom(shiny,column)
importFrom(shiny,conditionalPanel)
importFrom(shiny,div)
importFrom(shiny,downloadButton)
importFrom(shiny,downloadHandler)
importFrom(shiny,downloadLink)
importFrom(shiny,fileInput)
importFrom(shiny,fixedRow)
importFrom(shiny,fluidPage)
importFrom(shiny,fluidRow)
importFrom(shiny,h1)
importFrom(shiny,h2)
importFrom(shiny,h3)
importFrom(shiny,h4)
importFrom(shiny,h5)
importFrom(shiny,helpText)
importFrom(shiny,hideTab)
importFrom(shiny,hoverOpts)
importFrom(shiny,hr)
importFrom(shiny,icon)
importFrom(shiny,includeCSS)
importFrom(shiny,includeScript)
importFrom(shiny,isRunning)
importFrom(shiny,isolate)
importFrom(shiny,mainPanel)
importFrom(shiny,modalButton)
importFrom(shiny,modalDialog)
importFrom(shiny,navbarMenu)
importFrom(shiny,navbarPage)
importFrom(shiny,nearPoints)
importFrom(shiny,numericInput)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,p)
importFrom(shiny,parseQueryString)
importFrom(shiny,plotOutput)
importFrom(shiny,radioButtons)
importFrom(shiny,reactive)
importFrom(shiny,reactiveValues)
importFrom(shiny,removeModal)
importFrom(shiny,renderPlot)
importFrom(shiny,renderTable)
importFrom(shiny,renderText)
importFrom(shiny,renderUI)
importFrom(shiny,runApp)
importFrom(shiny,safeError)
importFrom(shiny,selectInput)
importFrom(shiny,selectizeInput)
importFrom(shiny,shinyApp)
importFrom(shiny,shinyUI)
importFrom(shiny,showModal)
importFrom(shiny,showTab)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,sliderInput)
importFrom(shiny,span)
importFrom(shiny,stopApp)
importFrom(shiny,tabPanel)
importFrom(shiny,tableOutput)
importFrom(shiny,tabsetPanel)
importFrom(shiny,tag)
importFrom(shiny,tagAppendAttributes)
importFrom(shiny,tagAppendChild)
importFrom(shiny,tagAppendChildren)
importFrom(shiny,tagList)
importFrom(shiny,tags)
importFrom(shiny,textAreaInput)
importFrom(shiny,textInput)
importFrom(shiny,textOutput)
importFrom(shiny,uiOutput)
importFrom(shiny,updateCheckboxInput)
importFrom(shiny,updateNumericInput)
importFrom(shiny,updateSelectizeInput)
importFrom(shiny,updateSliderInput)
importFrom(shiny,updateTabsetPanel)
importFrom(shiny,updateTextInput)
importFrom(shiny,wellPanel)
importFrom(shinyBS,bsCollapse)
importFrom(shinyBS,bsCollapsePanel)
importFrom(shinyBS,bsPopover)
importFrom(shinyBS,bsTooltip)
importFrom(shinyBS,updateCollapse)
importFrom(shinyjs,addClass)
importFrom(shinyjs,disable)
importFrom(shinyjs,disabled)
importFrom(shinyjs,enable)
importFrom(shinyjs,hidden)
importFrom(shinyjs,hide)
importFrom(shinyjs,onclick)
importFrom(shinyjs,removeClass)
importFrom(shinyjs,runjs)
importFrom(shinyjs,show)
importFrom(shinyjs,toggle)
importFrom(shinyjs,toggleClass)
importFrom(shinyjs,toggleElement)
importFrom(shinyjs,toggleState)
importFrom(shinyjs,useShinyjs)
importFrom(stats,IQR)
importFrom(stats,anova)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,cor.test)
importFrom(stats,density)
importFrom(stats,fisher.test)
importFrom(stats,fligner.test)
importFrom(stats,formula)
importFrom(stats,kmeans)
importFrom(stats,kruskal.test)
importFrom(stats,lm)
importFrom(stats,loess.smooth)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,optim)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,prcomp)
importFrom(stats,setNames)
importFrom(stats,t.test)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(stringr,str_match)
importFrom(stringr,str_split)
importFrom(stringr,str_split_fixed)
importFrom(survival,Surv)
importFrom(survival,coxph)
importFrom(survival,survdiff)
importFrom(survival,survfit)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(utils,askYesNo)
importFrom(utils,download.file)
importFrom(utils,head)
importFrom(utils,packageVersion)
importFrom(utils,read.delim)
importFrom(utils,read.table)
importFrom(utils,setTxtProgressBar)
importFrom(utils,txtProgressBar)
importFrom(utils,untar)
importFrom(utils,unzip)
importFrom(utils,write.table)
importFrom(xtable,print.xtable)
importFrom(xtable,xtable)
useDynLib(psichomics, .registration=TRUE)
