calcNearestStringDist   Calculate distances to the nearest string
calculateFitnessScore   Calculate fitness scores.
calculateRelativeFC     Calculate logFCs relative to WT using edgeR
collapseMutantsBySimilarity
                        Collapse mutants by similarity
digestFastqs            Read, filter and digest sequences from fastq
                        file(s).
generateQCReport        Generate QC report
groupSimilarSequences   Create a conversion table for collapsing
                        similar sequences
linkMultipleVariants    Process an experiment with multiple variable
                        sequences
plotDistributions       Plot distribution of observed values
plotFiltering           Visualize the filtering procedure
plotMeanDiff            Construct an MA (mean-difference) plot
plotPairs               Make pairs plot of selected assay from a
                        SummarizedExperiment object
plotTotals              Plot the column totals of a selected assay
plotVolcano             Construct a volcano plot
relabelMutPositions     Relabel the positions of mutations in the
                        designated ID
summarizeExperiment     Summarize and collapse multiple mutational
                        scanning experiments
