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