# Generated by roxygen2: do not edit by hand

S3method(merge,CircSeqAlignTkSim)
S3method(plot,CircSeqAlignTkCoverage)
export(align_reads)
export(build_app)
export(build_index)
export(calc_coverage)
export(filter_reads)
export(generate_reads)
export(plot_coverage)
exportClasses(CircSeqAlignTkAlign)
exportClasses(CircSeqAlignTkCoverage)
exportClasses(CircSeqAlignTkRefIndex)
exportClasses(CircSeqAlignTkSim)
importFrom(BiocGenerics,width)
importFrom(Biostrings,BStringSet)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(Biostrings,reverseComplement)
importFrom(Biostrings,writeXStringSet)
importFrom(IRanges,IRanges)
importFrom(IRanges,coverage)
importFrom(R.utils,bunzip2)
importFrom(R.utils,bzip2)
importFrom(R.utils,gunzip)
importFrom(R.utils,gzip)
importFrom(Rbowtie2,bowtie2)
importFrom(Rbowtie2,bowtie2_build)
importFrom(Rbowtie2,remove_adapters)
importFrom(Rhisat2,hisat2)
importFrom(Rhisat2,hisat2_build)
importFrom(Rsamtools,BamFile)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,asBam)
importFrom(Rsamtools,filterBam)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBam)
importFrom(Rsamtools,sortBam)
importFrom(S4Vectors,FilterRules)
importFrom(ShortRead,FastqStreamer)
importFrom(ShortRead,ShortReadQ)
importFrom(ShortRead,writeFastq)
importFrom(ShortRead,yield)
importFrom(dplyr,arrange)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,summarise)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,geom_area)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,xlim)
importFrom(htmltools,tags)
importFrom(magrittr,"%>%")
importFrom(methods,getPackageName)
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,slot)
importFrom(parallel,detectCores)
importFrom(plotly,ggplotly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,renderPlotly)
importFrom(rlang,.data)
importFrom(shiny,HTML)
importFrom(shiny,actionButton)
importFrom(shiny,column)
importFrom(shiny,div)
importFrom(shiny,fluidPage)
importFrom(shiny,fluidRow)
importFrom(shiny,h1)
importFrom(shiny,h2)
importFrom(shiny,h3)
importFrom(shiny,hr)
importFrom(shiny,icon)
importFrom(shiny,observe)
importFrom(shiny,observeEvent)
importFrom(shiny,p)
importFrom(shiny,reactive)
importFrom(shiny,reactiveValues)
importFrom(shiny,renderPrint)
importFrom(shiny,renderTable)
importFrom(shiny,renderText)
importFrom(shiny,runApp)
importFrom(shiny,selectInput)
importFrom(shiny,shinyApp)
importFrom(shiny,sliderInput)
importFrom(shiny,stopApp)
importFrom(shiny,tabPanel)
importFrom(shiny,tableOutput)
importFrom(shiny,tabsetPanel)
importFrom(shiny,textInput)
importFrom(shiny,titlePanel)
importFrom(shiny,updateActionButton)
importFrom(shiny,verbatimTextOutput)
importFrom(shiny,wellPanel)
importFrom(shinyFiles,parseDirPath)
importFrom(shinyFiles,parseFilePaths)
importFrom(shinyFiles,shinyDirButton)
importFrom(shinyFiles,shinyDirChoose)
importFrom(shinyFiles,shinyFileChoose)
importFrom(shinyFiles,shinyFilesButton)
importFrom(shinyjs,disable)
importFrom(shinyjs,disabled)
importFrom(shinyjs,enable)
importFrom(shinyjs,extendShinyjs)
importFrom(shinyjs,hidden)
importFrom(shinyjs,js)
importFrom(shinyjs,showElement)
importFrom(shinyjs,useShinyjs)
importFrom(stats,rbinom)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(tidyr,pivot_longer)
importFrom(tools,file_ext)
importFrom(tools,file_path_sans_ext)
importFrom(utils,packageVersion)
importFrom(utils,write.table)
