Changes in version 0.99.1                        

  - Fix non-ASCII characters in CITATION file

                       Changes in version 0.99.0                        

  - Prepare for Bioconductor submission
  - Remove deprecated arguments variableCollapseMaxDist,
    variableCollapseMinReads and variableCollapseMinRatio from
    digestFastqs (deprecated in mutscan 0.3.0)

                        Changes in version 0.3.4                        

  - Allow use of scattermore/scattermost in plotPairs

                        Changes in version 0.3.3                        

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

                        Changes in version 0.3.1                        

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

                        Changes in version 0.3.0                        

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

                       Changes in version 0.2.37                        

  - accommodate changes in edgeR version 3.42 (Bioconductor 3.17)
  - mutscan manuscript published and available at
    https://doi.org/10.1186/s13059-023-02967-0

                       Changes in version 0.2.36                        

  - Check that reads don't exceed the maximal allowed length
  - Add parameter to specify maximal read length

                       Changes in version 0.2.35                        

  - Add alternative names for variants (including HGVS identifiers)

                       Changes in version 0.2.34                        

  - Expand examples in function documentation

                       Changes in version 0.2.33                        

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

                       Changes in version 0.2.32                        

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

                       Changes in version 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

                       Changes in version 0.2.30                        

  - Swap to MIT license

                       Changes in version 0.2.29                        

  - Include degrees of freedom in output from calculateRelativeFC

                       Changes in version 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.

                       Changes in version 0.2.27                        

  - Add linkMultipleVariants function

                       Changes in version 0.2.26                        

  - Use arithmetic instead of geometric mean for PPI calculations

                       Changes in version 0.2.25                        

  - Only add names to WT sequences if they are unnamed

                       Changes in version 0.2.24                        

  - Added function to calculate nearest string distances

                       Changes in version 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()

                       Changes in version 0.2.22                        

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

                       Changes in version 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.