BadRegionFinder-package
                        BadRegionFinder: an R/Bioconductor package for
                        identifying regions with bad coverage
determineCoverage       Determines the coverage (recommended for
                        whole-genome analyses)
determineCoverageQuality
                        Classifies the determined coverage
determineQuantiles      Determines basewise user-defined quantiles
determineRegionsOfInterest
                        Determines the regions of interest
plotDetailed            Plots a more detailed overview of the coverage
                        quality
plotSummary             Plots a summary of the coverage quality
plotSummaryGenes        Plots a summary of the coverage quality
                        concerning the genes only
reportBadRegionsDetailed
                        Gives a detailed report on the coverage quality
reportBadRegionsGenes   Sums up the coverage quality on a gene basis
reportBadRegionsSummary
                        Sums up the coverage quality
