| Rqc-package | Quality Control Tool for High-Throughput Sequencing Data |
| 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. |
| perCycleBasecall | Class RqcResultSet |
| perCycleBasecall-method | Class RqcResultSet |
| perCycleQuality | Class RqcResultSet |
| perCycleQuality-method | Class RqcResultSet |
| perFileInformation | Class RqcResultSet |
| perFileInformation-method | Class RqcResultSet |
| perFileTopReads | Class RqcResultSet |
| perFileTopReads-method | Class RqcResultSet |
| perReadFrequency | Class RqcResultSet |
| perReadFrequency-method | Class RqcResultSet |
| perReadQuality | Class RqcResultSet |
| perReadQuality-method | Class RqcResultSet |
| perReadWidth | Class RqcResultSet |
| perReadWidth-method | Class RqcResultSet |
| Rqc | Quality Control Tool for High-Throughput Sequencing Data |
| rqc | Main Rqc function |
| rqcCycleAverageQualityCalc | Per cycle average quality by files |
| rqcCycleAverageQualityPcaCalc | Biplot of PCA of per cycle read average quality |
| rqcCycleAverageQualityPcaPlot | Biplot of PCA of per cycle read average quality |
| rqcCycleAverageQualityPlot | Per cycle average quality by files |
| rqcCycleBaseCallsCalc | Per cycle base calls plot |
| rqcCycleBaseCallsLinePlot | Per cycle base calls plot |
| rqcCycleBaseCallsPlot | Per cycle base calls plot |
| rqcCycleGCCalc | Per cycle percentual GC plot |
| rqcCycleGCPlot | Per cycle percentual GC plot |
| rqcCycleQualityBoxCalc | Per cycle quality box plot |
| rqcCycleQualityBoxPlot | Per cycle quality box plot |
| rqcCycleQualityCalc | Per cycle quality plot |
| rqcCycleQualityPlot | Per cycle quality plot |
| rqcFileHeatmap | Heatmap of distance matrix of top over-represented reads |
| rqcGroupCycleAverageQualityCalc | Per group average quality across cycles |
| rqcGroupCycleAverageQualityPlot | Per group average quality across cycles |
| rqcQA | Quality Assessment Rqc function |
| rqcQA-method | Quality Assessment Rqc function |
| rqcReadFrequencyCalc | Read frequency plot |
| rqcReadFrequencyPlot | Read frequency plot |
| rqcReadQualityBoxCalc | Per read mean quality box plot |
| rqcReadQualityBoxPlot | Per read mean quality box plot |
| rqcReadQualityCalc | Per read quality plot |
| rqcReadQualityPlot | Per read quality plot |
| rqcReadWidthCalc | Per read width plot |
| rqcReadWidthPlot | Per read width plot |
| rqcReport | Quality Control HTML Report |
| RqcResultSet-class | Class RqcResultSet |
| 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 |