# Generated by roxygen2: do not edit by hand

export(checkpoint)
export(detectFileFormat)
export(fromRRDNA)
export(matdist)
export(rqc)
export(rqcCycleAverageQualityCalc)
export(rqcCycleAverageQualityPcaCalc)
export(rqcCycleAverageQualityPcaPlot)
export(rqcCycleAverageQualityPlot)
export(rqcCycleBaseCallsCalc)
export(rqcCycleBaseCallsLinePlot)
export(rqcCycleBaseCallsPlot)
export(rqcCycleGCCalc)
export(rqcCycleGCPlot)
export(rqcCycleQualityBoxCalc)
export(rqcCycleQualityBoxPlot)
export(rqcCycleQualityCalc)
export(rqcCycleQualityPlot)
export(rqcFileHeatmap)
export(rqcGroupCycleAverageQualityCalc)
export(rqcGroupCycleAverageQualityPlot)
export(rqcReadFrequencyCalc)
export(rqcReadFrequencyPlot)
export(rqcReadQualityBoxCalc)
export(rqcReadQualityBoxPlot)
export(rqcReadQualityCalc)
export(rqcReadQualityPlot)
export(rqcReadWidthCalc)
export(rqcReadWidthPlot)
export(rqcReport)
export(rqcShinyReport)
export(stats4trim)
export(subsetByGroup)
export(subsetByPair)
export(toRRDNA)
exportClasses(RqcResultSet)
exportMethods(perCycleBasecall)
exportMethods(perCycleQuality)
exportMethods(perFileInformation)
exportMethods(perFileTopReads)
exportMethods(perReadFrequency)
exportMethods(perReadQuality)
exportMethods(perReadWidth)
exportMethods(rqcQA)
import(methods)
importClassesFrom(ShortRead,.QA)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,multicoreWorkers)
importFrom(BiocStyle,markdown)
importFrom(GenomicFiles,REDUCEsampler)
importFrom(GenomicFiles,reduceByYield)
importFrom(Rsamtools,"yieldSize<-")
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,scanBam)
importFrom(ShortRead,FastqFile)
importFrom(ShortRead,FastqSampler)
importFrom(biovizBase,colorBlindSafePal)
importFrom(biovizBase,getBioColor)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_continuous)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_x_discrete)
importFrom(ggplot2,scale_x_log10)
importFrom(grid,arrow)
importFrom(grid,unit)
importFrom(knitr,kable)
importFrom(knitr,knit)
importFrom(markdown,markdownToHTML)
importFrom(plyr,ddply)
importFrom(plyr,summarize)
importFrom(reshape2,dcast)
importFrom(reshape2,melt)
importFrom(shiny,checkboxGroupInput)
importFrom(shiny,fluidPage)
importFrom(shiny,mainPanel)
importFrom(shiny,need)
importFrom(shiny,plotOutput)
importFrom(shiny,renderPlot)
importFrom(shiny,renderTable)
importFrom(shiny,runApp)
importFrom(shiny,selectInput)
importFrom(shiny,sidebarLayout)
importFrom(shiny,sidebarPanel)
importFrom(shiny,tabPanel)
importFrom(shiny,tableOutput)
importFrom(shiny,tabsetPanel)
importFrom(shiny,titlePanel)
importFrom(shiny,validate)
importFrom(stats,hclust)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(utils,browseURL)
importFrom(utils,head)
importFrom(utils,packageVersion)
importMethodsFrom(BiocGenerics,width)
importMethodsFrom(BiocParallel,bpmapply)
importMethodsFrom(Biostrings,encoding)
importMethodsFrom(Biostrings,quality)
importMethodsFrom(GenomicAlignments,readGAlignments)
importMethodsFrom(S4Vectors,Rle)
importMethodsFrom(S4Vectors,mcols)
importMethodsFrom(ShortRead,FastqStreamer)
importMethodsFrom(ShortRead,ShortReadQ)
importMethodsFrom(ShortRead,alphabetByCycle)
importMethodsFrom(ShortRead,alphabetScore)
importMethodsFrom(ShortRead,countLines)
importMethodsFrom(ShortRead,sread)
importMethodsFrom(ShortRead,yield)
useDynLib(Rqc)
