Rqc-package             Quality Control Tool for High-Throughput
                        Sequencing Data
RqcResultSet-class      Class RqcResultSet
checkpoint              Save time storing longer analysis step on disk
detectFileFormat        Detect file format
fromRRDNA               Revert codified DNA sequences to original DNA
                        sequences.
matdist                 Distance matrix of the similarity between the
                        DNA sequences.
rqc                     Main Rqc function
rqcCycleAverageQualityCalc
                        Per cycle average quality by files
rqcCycleAverageQualityPcaCalc
                        Biplot of PCA of per cycle read average quality
rqcCycleBaseCallsCalc   Per cycle base calls plot
rqcCycleGCCalc          Per cycle percentual GC plot
rqcCycleQualityBoxCalc
                        Per cycle quality box plot
rqcCycleQualityCalc     Per cycle quality plot
rqcFileHeatmap          Heatmap of distance matrix of top
                        over-represented reads
rqcGroupCycleAverageQualityCalc
                        Per group average quality across cycles
rqcQA                   Quality Assessment Rqc function
rqcReadFrequencyCalc    Read frequency plot
rqcReadQualityBoxCalc   Per read mean quality box plot
rqcReadQualityCalc      Per read quality plot
rqcReadWidthCalc        Per read width plot
rqcReport               Quality Control HTML Report
rqcShinyReport          Interactive Quality Control Report
stats4trim              Minimun read mean quality and maximum
                        percentage loss of reads estimations for
                        trimming step.
subsetByGroup           Subset RqcResultSet object by group name.
subsetByPair            Subset RqcResultSet object by pair files.
toRRDNA                 Title: Convert DNA sequences to Reduced
                        Representation format
