import(methods)
import(BiocGenerics)
import(IRanges)
importFrom("graphics", "plot", "lines")
importFrom("MASS", "isoMDS")
importFrom("BSgenome", "available.genomes")
importFrom("GenomicRanges", "seqlengths")

exportMethods(alignPeaks, extendRanges, filterDuplReads, mergeRegions, enrichedRegions, enrichedPeaks, stdPeakLocation, PeakLocation, listOverlap, tabDuplReads, cmds, cmdsFit, islandCounts, ssdCoverage, giniCoverage, regionsCoverage, stdGrid, plot, lines, enrichedChrRegions, countHitsWindow, getViewsInfo, getCover, plotMeanCoverage, findPeakHeight)
export(fdrEnrichedCounts, gridCoverage, plotChrRegions, coverageDiff, rowLogRegLRT, plotminHeight)

exportClasses("cmdsFit","gridCover")
