# Generated by roxygen2: do not edit by hand

export(TargetExperiment)
export(TargetExperimentList)
export(checkBedFasta)
export(pileupCounts)
exportClasses(TargetExperiment)
exportClasses(TargetExperimentList)
S3method(plot, TargetExperiment)
S3method(plot, TargetExperimentList)
export(plot.TargetExperiment)
export(plot.TargetExperimentList)
exportMethods("setAttribute<-")
exportMethods("setBamFile<-")
exportMethods("setBedFile<-")
exportMethods("setFastaFile<-")
exportMethods("setFeature<-")
exportMethods("setFeaturePanel<-")
exportMethods("setGenePanel<-")
exportMethods("setPileupP<-")
exportMethods("setScanBamP<-")
exportMethods(addStatSummSheet)
exportMethods(biasExploration)
exportMethods(buildFeaturePanel)
exportMethods(buildReport)
exportMethods(getAttribute)
exportMethods(getBamFile)
exportMethods(getBedFile)
exportMethods(getFastaFile)
exportMethods(getFeature)
exportMethods(getFeaturePanel)
exportMethods(getGenePanel)
exportMethods(getLowCtsFeatures)
exportMethods(getOverlappedRegions)
exportMethods(getPanels)
exportMethods(getPileupP)
exportMethods(getRegion)
exportMethods(getScanBamP)
exportMethods(ggplotColours)
exportMethods(initialize)
exportMethods(plotAttrExpl)
exportMethods(plotAttrPerform)
exportMethods(plotFeatPerform)
exportMethods(plotFeature)
exportMethods(plotGeneAttrPerFeat)
exportMethods(plotGlobalAttrExpl)
exportMethods(plotInOutFeatures)
exportMethods(plotMetaDataExpl)
exportMethods(plotNtdPercentage)
exportMethods(plotPoolPerformance)
exportMethods(plotRegion)
exportMethods(print)
exportMethods(readFrequencies)
exportMethods(show)
exportMethods(summarizePanel)
exportMethods(summary)
exportMethods(summaryFeatureLev)
exportMethods(summaryGeneLev)
exportMethods(summaryIntervals)
import(BiocParallel)
import(GenomicRanges)
import(Rsamtools)
import(ggplot2)
import(methods)
import(openxlsx)
import(plyr)
importClassesFrom(IRanges,IRanges)
importClassesFrom(S4Vectors,Rle)
importFrom(Biostrings,letterFrequency)
importFrom(Hmisc,capitalize)
importFrom(IRanges,IRanges)
importFrom(graphics,"plot")
importFrom(cowplot,plot_grid)
importFrom(reshape2,melt)
importFrom(grDevices, colorRampPalette, hcl)
importFrom(stats, IQR, aggregate, median, sd)
importFrom(utils, head, read.delim, tail)
importMethodsFrom(BiocGenerics,strand)
importMethodsFrom(BiocParallel,"bpprogressbar<-")
importMethodsFrom(BiocParallel,bplapply)
importMethodsFrom(BiocParallel,bpmapply)
importMethodsFrom(BiocParallel,bpworkers)
importMethodsFrom(GenomeInfoDb,"seqnames<-")
importMethodsFrom(GenomeInfoDb,seqlengths)
importMethodsFrom(GenomeInfoDb,seqlevels)
importMethodsFrom(GenomeInfoDb,seqnames)
importMethodsFrom(GenomicAlignments,readGAlignments)
importMethodsFrom(S4Vectors,Rle)
importMethodsFrom(S4Vectors,runValue)
