analyzeDuprates         Read in a BAM file and count the tags falling
                        on the features described in the GTF file
bamutilMarkDuplicates   Mark duplicates using bamutil
cumulativeDuprateBarplot
                        Barplot showing the cumulative read counts
                        fraction
dm                      Duplication matrix of a good RNASeq experiment
dm.bad                  Duplication matrix of a failed RNASeq
                        experiment
dupRadar                dupRadar.
dupRadar_examples       Example data containing precomputed matrices
                        for two RNASeq experiments
duprateExpBoxplot       Duplication rate ~ total reads per kilobase
                        (RPK) boxplot
duprateExpDensPlot      Duplication rate ~ total read count plot
duprateExpFit           Duplication rate ~ total read count fit model
duprateExpIdentify      Identify genes plotted by 'duprateExpPlot'
duprateExpPlot          Duplication rate ~ total read count plot
expressionHist          Draw histogram with the expression values
getBinDuplication       Helper function used in 'duprateExpBoxplot'
getBinRpkMean           Helper function used in 'duprateExpBoxplot'
getDupMatBin            Helper function used in 'getBinDuplication' and
                        'getBinRpkMean'
getDupMatStats          Report duplication stats on regions
getDynamicRange         Dynamic range
getRpkBinReadCountFraction
                        Helper function used in
                        'readcountExpressionBoxplot'
getRpkCumulativeReadCountFraction
                        Helper function used in
                        'readcountExpressionBoxplot'
markDuplicates          Program dispatchers to mark duplicated reads
                        from a BAM file
picardMarkDuplicates    Mark duplicates using Picard tools
readcountExpBoxplot     Barplot of percentage of reads falling into
                        expression bins
