NEWS.md

In js2264/periodicDNA: Set of tools to identify periodic occurrences of k-mers in DNA sequences

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

js2264/periodicDNA documentation built on Nov. 3, 2022, 10:47 p.m.