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 |