Changelog

Source: NEWS.md

periodicDNA 0.3.2 (dev)

  • IMPORTANT:
    • Implemented data-raw for reproducibility
  • MINOR:
    • Changed xlim of norm. distr. plot in plotPeriodicityResults()

periodicDNA 0.3.1 (2020-05-05)

  • IMPORTANT:
    • rollmean(k=3) is now applied before normalisation as well, on the raw distribution vector
    • plotPeriodicityResults() output returns one single plot (with cowplot)
    • getPeriodicityTrack() now returns the Rle
    • Improved plotting functions -now show shuffled for plotPeriodicityResults()
    • Added ggplot2 theming
  • MINOR:
    • Changed many variable names (all to snake_case)
    • sampleGRanges is now full-fledged function (GRanges, DNAStringSet, character and BSgenome methods)
    • sampleGenome is an alias for sampleGRanges.character
    • Added sacCer3 to getPeriodicity BSgenomes
    • Added DNAString method for getPeriodicity
    • Added a vignette describing the internal steps
    • Clarified user-level functions in README
    • Added ce11_TSSs data
    • Renamed generateperiodicitytrack as getPeriodicityTrack
    • Renamed variables in getFPI and getPeriodicity
    • Created a utility char2BSgenome()

periodicDNA 0.3.0 (2020-05-03)

  • Added tests
  • Added getFPI function
  • cleaned-up functions
  • cleaned-up function dependencies
  • Added toy data
  • Added vignette

periodicDNA 0.2.1 (2020-03-04)

  • Added Travis build check
  • Simplified README.md