# Generated by roxygen2: do not edit by hand

export(SummarizedExomePeak)
export(exomePeak2)
export(scanMeripBAM)
exportClasses(MeripBamFileList)
exportClasses(SummarizedExomePeak)
exportMethods("GCsizeFactors<-")
exportMethods("exomePeak2Results<-")
exportMethods(GCsizeFactors)
exportMethods(LibraryType)
exportMethods(Parameter)
exportMethods(Results)
exportMethods(estimateSeqDepth)
exportMethods(exomePeak2Results)
exportMethods(exomePeakCalling)
exportMethods(exportResults)
exportMethods(glmDM)
exportMethods(glmM)
exportMethods(normalizeGC)
exportMethods(plotExonLength)
exportMethods(plotLfcGC)
exportMethods(plotReadsGC)
exportMethods(plotSizeFactors)
import(BSgenome)
import(DESeq2)
import(GenomicAlignments)
import(GenomicFeatures)
import(GenomicRanges)
import(SummarizedExperiment)
import(apeglm)
import(cqn)
import(ggplot2)
importFrom(BSgenome,getBSgenome)
importFrom(Biobase,package.version)
importFrom(BiocParallel,MulticoreParam)
importFrom(BiocParallel,SerialParam)
importFrom(BiocParallel,SnowParam)
importFrom(BiocParallel,register)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,startIndex)
importFrom(DESeq2,DESeqDataSet)
importFrom(DESeq2,estimateDispersions)
importFrom(DESeq2,estimateSizeFactors)
importFrom(DESeq2,estimateSizeFactorsForMatrix)
importFrom(DESeq2,nbinomWaldTest)
importFrom(DESeq2,results)
importFrom(GenomeInfoDb,"seqlengths<-")
importFrom(GenomeInfoDb,seqlengths)
importFrom(GenomicAlignments,summarizeOverlaps)
importFrom(GenomicFeatures,exons)
importFrom(GenomicFeatures,exonsBy)
importFrom(IRanges,IRanges)
importFrom(IRanges,subsetByOverlaps)
importFrom(Rsamtools,"index<-")
importFrom(Rsamtools,"yieldSize<-")
importFrom(Rsamtools,BamFileList)
importFrom(Rsamtools,ScanBamParam)
importFrom(Rsamtools,asMates)
importFrom(Rsamtools,indexBam)
importFrom(Rsamtools,scanBamFlag)
importFrom(Rsamtools,sortBam)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,na.omit)
importFrom(S4Vectors,queryHits)
importFrom(S4Vectors,subjectHits)
importFrom(genefilter,filtered_R)
importFrom(genefilter,filtered_p)
importFrom(mclust,densityMclust)
importFrom(methods,as)
importFrom(methods,is)
importFrom(methods,new)
importFrom(reshape2,melt)
importFrom(rtracklayer,asGFF)
importFrom(rtracklayer,export)
importFrom(rtracklayer,path)
importFrom(stats,pbinom)
importFrom(stats,qbinom)
importFrom(stats,relevel)
importFrom(utils,capture.output)
importFrom(utils,read.table)
importFrom(utils,write.csv)
