import(methods, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments)

importMethodsFrom(rtracklayer, browserSession,
                 browserView, export, genome,
                 "genome<-", import, ranges,
                 "track<-", trackNames)

importFrom(graphics, abline, legend, lines, plot)

importFrom(grDevices, col2rgb, dev.off, pdf)

importFrom(rtracklayer, SeqinfoForUCSCGenome)

importFrom(stats, p.adjust, pnorm, rgamma, rpois, runif)

export(
	addDummyProb,
	addPseudoAlignment,
        annotateRIP,
        binCount,
        combineAlignGals,
        computeLogOdd,
        computeRPKM,
	combineRIP,
        disambiguateMultihits,
        empiricalFDR,
        evalBinSize,
        exportGRanges,
        galp2gal,
        getAlignGal,
        logScoreWithControl,
        logScoreWithoutControl,
	mainSeekSingleChrom,
        mainSeek,
        nbh,
        nbh.GRanges,
        nbh.integer,
        nbh_chk,
        nbh_em,
        nbh_gen,
        nbh_init,
        nbh_vit,
        nbm_chk,
        nbm_em,
        plotCoverage,
        plotStrandedCoverage,
        randindx,
        ripSeek,
        rulebaseRIPSeek,
        scoreMergedBins,
        seekRIP,
        selectBinSize,
        statdis,
        viewRIP
)
