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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("bamFile<-")
export("condition<-")
export("dontWriteHDF5<-")
export("featureExclusionMask<-")
export("method<-")
export("name<-")
export("nonSplicedReads<-")
export("parallel<-")
export("samples<-")
export("scanBamParam<-")
export("strandSpecific<-")
export("verbose<-")
export("workingDir<-")
export()
export(FraseR)
export(FraseRDataSet)
export(FraseRShinyApp)
export(aberrant)
export(annotateRanges)
export(bamFile)
export(calculatePSIValues)
export(calculatePValues)
export(calculateZScores)
export(cleanCache)
export(condition)
export(countRNAData)
export(cpp_truncGrad_db)
export(cpp_truncNll_db)
export(createTestFraseRDataSet)
export(createTestFraseRSettings)
export(dontWriteHDF5)
export(featureExclusionMask)
export(filterExpression)
export(fitAutoencoder)
export(loadFraseRDataSet)
export(makeExampleFraseRDataSet)
export(makeSimulatedFraserDataSet_BetaBinomial)
export(mapSeqlevels)
export(method)
export(na2default)
export(na2false)
export(na2zero)
export(name)
export(nonSplicedReads)
export(null2default)
export(null2na)
export(parallel)
export(plotAberrantPerSample)
export(plotCountCorHeatmap)
export(plotFilterExpression)
export(plotJunctionDistribution)
export(plotSampleResults)
export(plotVolcano)
export(pseudocount)
export(psiTypes)
export(results)
export(samples)
export(saveFraseRDataSet)
export(scanBamParam)
export(strandSpecific)
export(verbose)
export(workingDir)
exportMethods("bamFile<-")
exportMethods("condition<-")
exportMethods("method<-")
exportMethods("name<-")
exportMethods("nonSplicedReads<-")
exportMethods("parallel<-")
exportMethods("samples<-")
exportMethods("scanBamParam<-")
exportMethods("strandSpecific<-")
exportMethods("workingDir<-")
exportMethods(bamFile)
exportMethods(condition)
exportMethods(method)
exportMethods(name)
exportMethods(nonSplicedReads)
exportMethods(parallel)
exportMethods(results)
exportMethods(samples)
exportMethods(scanBamParam)
exportMethods(strandSpecific)
exportMethods(workingDir)
import(BiocParallel)
import(GenomicAlignments)
import(GenomicRanges)
import(SummarizedExperiment)
import(tidyr)
importFrom(BBmisc,"%nin%")
importFrom(BBmisc,chunk)
importFrom(BBmisc,is.error)
importFrom(BBmisc,isFALSE)
importFrom(BBmisc,isScalarCharacter)
importFrom(BBmisc,isScalarInteger)
importFrom(BBmisc,isScalarLogical)
importFrom(BBmisc,isScalarNumeric)
importFrom(BBmisc,isScalarValue)
importFrom(BiocGenerics,counts)
importFrom(BiocGenerics,updateObject)
importFrom(DT,dataTableOutput)
importFrom(DT,renderDataTable)
importFrom(DelayedArray,"path<-")
importFrom(DelayedArray,rowMaxs)
importFrom(DelayedArray,rowMeans)
importFrom(DelayedMatrixStats,colMeans2)
importFrom(DelayedMatrixStats,rowMeans2)
importFrom(DelayedMatrixStats,rowMedians)
importFrom(DelayedMatrixStats,rowQuantiles)
importFrom(DelayedMatrixStats,rowSds)
importFrom(GenomeInfoDb,"seqlevels<-")
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomeInfoDb,seqlevels)
importFrom(HDF5Array,path)
importFrom(HDF5Array,writeHDF5Array)
importFrom(IRanges,IRanges)
importFrom(IRanges,from)
importFrom(IRanges,subsetByOverlaps)
importFrom(IRanges,to)
importFrom(LSD,colorpalette)
importFrom(LSD,heatscatter)
importFrom(MASS,bandwidth.nrd)
importFrom(MASS,kde2d)
importFrom(PRROC,pr.curve)
importFrom(R.utils,renameFile)
importFrom(R.utils,withTimeout)
importFrom(RColorBrewer,brewer.pal)
importFrom(Rsamtools,"bamWhich<-")
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,bamMapqFilter)
importFrom(Rsamtools,bamWhich)
importFrom(Rsamtools,scanBamHeader)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(VGAM,Coef)
importFrom(VGAM,betabinomial)
importFrom(VGAM,dbetabinom)
importFrom(VGAM,dbetabinom.ab)
importFrom(VGAM,pbetabinom)
importFrom(VGAM,pbetabinom.ab)
importFrom(VGAM,rbetabinom)
importFrom(VGAM,vglm)
importFrom(biomaRt,getBM)
importFrom(biomaRt,useEnsembl)
importFrom(data.table,":=")
importFrom(data.table,as.data.table)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,is.data.table)
importFrom(data.table,rbindlist)
importFrom(data.table,setnames)
importFrom(extraDistr,rdirmnom)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_histogram)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_discrete)
importFrom(ggplot2,scale_color_gradientn)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggpubr,ggarrange)
importFrom(gplots,col2hex)
importFrom(grDevices,adjustcolor)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,grid)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,polygon)
importFrom(graphics,text)
importFrom(graphics,title)
importFrom(htmlwidgets,saveWidget)
importFrom(keras,callback_early_stopping)
importFrom(keras,callback_terminate_on_naan)
importFrom(keras,constraint_minmaxnorm)
importFrom(keras,custom_metric)
importFrom(keras,get_weights)
importFrom(keras,k_exp)
importFrom(keras,k_log)
importFrom(keras,k_mean)
importFrom(keras,k_variable)
importFrom(keras,keras_model)
importFrom(keras,layer_dense)
importFrom(keras,layer_input)
importFrom(keras,layer_lambda)
importFrom(keras,optimizer_adam)
importFrom(keras,regularizer_l2)
importFrom(keras,set_weights)
importFrom(keras,use_python)
importFrom(methods,"slot<-")
importFrom(methods,as)
importFrom(methods,callNextMethod)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(methods,validObject)
importFrom(parallel,mclapply)
importFrom(pcaMethods,loadings)
importFrom(pcaMethods,pca)
importFrom(pheatmap,pheatmap)
importFrom(plotly,add_trace)
importFrom(plotly,event_data)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(plotly,plot_ly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,renderPlotly)
importFrom(plotly,subplot)
importFrom(rhdf5,H5Fclose)
importFrom(rhdf5,H5Fopen)
importFrom(rhdf5,h5ls)
importFrom(shiny,column)
importFrom(shiny,fluidPage)
importFrom(shiny,fluidRow)
importFrom(shiny,h1)
importFrom(shiny,h3)
importFrom(shiny,htmlOutput)
importFrom(shiny,mainPanel)
importFrom(shiny,navbarPage)
importFrom(shiny,numericInput)
importFrom(shiny,p)
importFrom(shiny,plotOutput)
importFrom(shiny,reactive)
importFrom(shiny,renderPlot)
importFrom(shiny,renderPrint)
importFrom(shiny,renderText)
importFrom(shiny,renderUI)
importFrom(shiny,selectInput)
importFrom(shiny,shinyApp)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,tabPanel)
importFrom(shiny,textInput)
importFrom(shiny,titlePanel)
importFrom(stats,cor)
importFrom(stats,cutree)
importFrom(stats,dbinom)
importFrom(stats,dist)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,optim)
importFrom(stats,optimize)
importFrom(stats,p.adjust)
importFrom(stats,pbinom)
importFrom(stats,plogis)
importFrom(stats,ppoints)
importFrom(stats,predict)
importFrom(stats,qbeta)
importFrom(stats,qlogis)
importFrom(stats,quantile)
importFrom(stats,rbinom)
importFrom(stats,rlnorm)
importFrom(stats,rnbinom)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(tensorflow,install_tensorflow)
importFrom(tibble,as_tibble)
importFrom(tools,file_path_as_absolute)
importFrom(utils,browseURL)
importFrom(utils,capture.output)
importFrom(utils,sessionInfo)
useDynLib(FraseR)