NEWS

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mutscan 0.99.1

• Fix non-ASCII characters in CITATION file

mutscan 0.99.0

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

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

• 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

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.