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Changelog

mutscan 0.3.4

  • Allow use of scattermore/scattermost in plotPairs

mutscan 0.3.3

  • Bugfix in mergeReadPairPartial for situation where specified minMergedLength/maxMergedLength is larger than the total length of the two merged sequences

mutscan 0.3.1

  • Adapt summarizeExperiment to include errorStatistics in metadata(se)
  • Modify plotPairs to ignore NAs rather than give an error when calculating correlations

mutscan 0.3.0

  • Collapsing of variable sequences is no longer supported by digestFastqs. Use collapseMutantsBySimilarity() instead

mutscan 0.2.37

mutscan 0.2.36

  • Check that reads don’t exceed the maximal allowed length
  • Add parameter to specify maximal read length

mutscan 0.2.35

  • Add alternative names for variants (including HGVS identifiers)

mutscan 0.2.34

  • Expand examples in function documentation

mutscan 0.2.33

  • Replace Matrix.utils::aggregate.Matrix (removed from CRAN) by DelayedArray::rowsum

mutscan 0.2.32

  • Expand FASTQ file paths automatically
  • Filter out reads where the variable region is longer than the best matching WT sequence

mutscan 0.2.31

  • Add option to include identity line in pairs plots
  • Select points to label in result plots based on nominal p-value
  • Add option to manually set the correlation range for coloring pairs plots

mutscan 0.2.30

  • Swap to MIT license

mutscan 0.2.29

  • Include degrees of freedom in output from calculateRelativeFC

mutscan 0.2.28

  • Rename calculatePPIScore to calculateFitnessScore
  • Add amino acid-related information (AA sequence, mutant name, number of mutated amino acid) to digestFastqs output, propagate through summarizeExperiment and collapseMutantsByAA.

mutscan 0.2.27

  • Add linkMultipleVariants function

mutscan 0.2.26

  • Use arithmetic instead of geometric mean for PPI calculations

mutscan 0.2.25

  • Only add names to WT sequences if they are unnamed

mutscan 0.2.24

  • Added function to calculate nearest string distances

mutscan 0.2.23

  • Changed default value of forbidden codons to “”
  • Make result plots more flexible
  • Propagate information about the number of mutated bases/codons in summarizeExperiment()

mutscan 0.2.22

  • Added argument to specify the title of the QC report.
  • Internal refactoring of argument checking.

mutscan 0.2.21

  • Added a NEWS.md file to track changes to the package.
  • Added the generateQCReport() function.
  • Added functions to plot results from calculateRelativeFC().
  • Added functions to plot distributions of counts as well as total counts.