# Generated by roxygen2: do not edit by hand
export(deltaBIC)
export(normalizeCoverage)
export(plotFraction)
export(plotMadSeq)
export(plotMixture)
export(posterior)
export(prepareCoverageGC)
export(prepareHetero)
export(runMadSeq)
exportClasses(MadSeq)
exportMethods(deltaBIC)
exportMethods(plotFraction)
exportMethods(plotMadSeq)
exportMethods(plotMixture)
exportMethods(posterior)
exportMethods(summary)
import(BSgenome)
import(BSgenome.Hsapiens.UCSC.hg19)
import(Biostrings)
import(GenomicAlignments)
import(GenomicRanges)
import(IRanges)
import(Rsamtools)
import(S4Vectors)
import(VariantAnnotation)
import(coda)
import(methods)
import(rjags)
import(zlibbioc)
importFrom(vcfR,read.vcfR)
importFrom(GenomeInfoDb,keepStandardChromosomes)
importFrom(SummarizedExperiment,rowRanges)
importFrom(VGAM,dbetabinom.ab)
importFrom(grDevices,colors)
importFrom(grDevices,rgb)
importFrom(graphics,abline)
importFrom(graphics,axis)
importFrom(graphics,curve)
importFrom(graphics,hist)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,mtext)
importFrom(graphics,par)
importFrom(graphics,plot)
importFrom(graphics,points)
importFrom(graphics,text)
importFrom(preprocessCore,normalize.quantiles)
importFrom(rtracklayer,import)
importFrom(stats,dbeta)
importFrom(stats,density)
importFrom(stats,dnbinom)
importFrom(stats,loess)
importFrom(utils,read.table)
importFrom(utils,write.table)
importMethodsFrom(GenomeInfoDb,"seqlevels<-")
