importFrom("aods3", "AIC.aodml", "anova.aodml", "aodml")
importFrom("Biobase", "exprs", "exprs<-")
importFrom("DESeq2", 
            "counts", 
            "DESeqDataSetFromMatrix", 
            "estimateSizeFactors", 
            "sizeFactors",
            "sizeFactors<-")
importFrom("DSS", "dispersion", "estDispersion", "newSeqCountSet")
import("ggplot2")
importFrom("gplots", "heatmap.2")
importFrom("graphics", "par")
importFrom("grDevices", "adjustcolor", "dev.off", "palette", "png")
importFrom("matrixStats", "rowVars")
importFrom("stats",
            "anova",
            "as.dist", 
            "complete.cases", 
            "cor", 
            "median",
            "p.adjust",
            "prcomp",
            "reshape",
            "sd",
            "var")
importFrom("utils", "tail", "write.table","head","read.table")
importFrom("foreach", "foreach", "%dopar%")
importFrom("doParallel", "registerDoParallel")
importFrom("parallel", "detectCores")
importFrom("ade4","dudi.pca")
importFrom("shiny","selectizeInput","actionButton","br","brushOpts","brushedPoints","checkboxGroupInput",
           "checkboxInput","column","conditionalPanel","downloadButton","downloadHandler",
           "fluidPage","fluidRow","h1","h2","mainPanel","navbarPage","nearPoints",
           "numericInput","observeEvent","p","plotOutput","radioButtons","reactive",
           "reactiveValues","renderPlot","renderUI","selectInput","shinyApp","sidebarLayout",
           "sidebarPanel","sliderInput","strong","tabPanel","tagList","uiOutput","wellPanel")
importFrom("factoextra","get_pca_var")
importFrom("shinycssloaders","withSpinner")
importFrom("DT","renderDataTable","dataTableOutput","datatable")

export(diffExpressedVariants,
        kissplice2counts,
        qualityControl,
        writeOutputKissDE,
       kissDE,
       exploreResults)

S3method("print", "countsData")
S3method("print", "pval")
