Rqc-package             Quality Control Tool for High-Throughput
                        Sequencing Data
RqcResultSet-class      Quality control data
perCycleBasecall        Frequency distribution of cycle-specific base
                        call
perCycleQuality         Frequency distribution of cycle-specific
                        quality
perFileInformation      File information
perReadQuality          Frequency distribution of per read mean quality
perReadWidth            Frequency distribution of read width
rqc                     Main Rqc function
rqcCycleAverageQualityCalc
                        Per cycle average quality calculation
rqcCycleAverageQualityPcaCalc
                        PCA calculation of per cycle read average
                        quality
rqcCycleAverageQualityPcaPlot
                        Biplot of PCA of per cycle read average quality
rqcCycleAverageQualityPlot
                        Per cycle average quality plot
rqcCycleBaseCallsCalc   Per cycle base call calculation
rqcCycleBaseCallsLinePlot
                        Per cycle base calls line plot
rqcCycleBaseCallsPlot   Per cycle base calls plot
rqcCycleGCCalc          Per cycle percentual GC.
rqcCycleGCPlot          Per cycle percentual GC plot
rqcCycleQualityBoxCalc
                        Per cycle quality percentiles calculation for
                        boxplot
rqcCycleQualityBoxPlot
                        Per cycle quality box plot
rqcCycleQualityCalc     Per cycle quality calculation
rqcCycleQualityPlot     Per cycle quality plot
rqcQA                   Quality Assessment Rqc function
rqcReadQualityBoxCalc   Per read mean quality percentiles calculation
                        for boxplot
rqcReadQualityBoxPlot   Per read mean quality box plot
rqcReadQualityCalc      Per read quality calculation
rqcReadQualityPlot      Per read quality plot
rqcReadWidthCalc        Per read width calculation
rqcReadWidthPlot        Per read width plot
rqcReport               Quality Control HTML Report
stats4trim              Minimun read mean quality and maximum
                        percentage loss of reads estimations for
                        trimming step.
