Changes in version 1.11.3                        

  - add show_bin_legend argument to plotMotifHeatmaps (contributed by
    @danymukesha, PR #62)

                        Changes in version 1.9.1                        

  - adapt dumpJaspar to also work with JASPAR2024

                        Changes in version 1.7.1                        

  - allow modification of heatmap graphical parameters by forwarding ...
    argument in plotMotifHeatmaps to all calls to
    ComplexHeatmap::Heatmap

                        Changes in version 1.3.1                        

  - update citation information

                        Changes in version 1.1.2                        

  - added citation to the Bioinformatics publication

                        Changes in version 1.1.1                        

  - added link to pre-print manuscript on biorXiv to README.md
  - added warning to bin(..., minAbsX = val) if adjusted zero-bin breaks
    deviate more than 20% from val
  - added doPlot argument to plotMotifHeatmaps to select if heatmaps
    should be plotted or just generated and returned
  - added LICENSE.md file
  - expanded monaLisa.Rmd vignette with illustration on how to do a
    binary or single set motif enrichment analysis
  - expanded on collineairty in regression in the
    selecting_motifs_with_randLassoStabSel.Rmd vignette and the choice
    of parameter values in stability selection.
  - updated the results.binned_6mer_enrichment_LMRs.rds and
    results.binned_motif_enrichment_LMRs.rds files stored in monaLisa
    under the current version of the package.

                        Changes in version 1.0.0                        

  - Initial release of monaLisa as part of Bioconductor 3.14

                       Changes in version 0.99.5                        

  - Updated R/monaLisa-package.R file

                       Changes in version 0.99.4                        

  - Suppressed warnings from matchPWM (due to presence of Ns) in
    regression vignette

                       Changes in version 0.99.3                        

  - Updated README.md file

                       Changes in version 0.99.2                        

  - Added fixes to the regression vignette
  - Addressed failing test in calcBinnedKmerEnr

                       Changes in version 0.99.1                        

  - Added examples where missing for exported functions
  - Harmonized function naming (anno_seqlogo -> annoSeqlogo,
    sample_random_regions -> sampleRandomRegions)
  - Clarified details on Pearson residual calculation
  - Adapted documentation for new version of BiocParallel
  - Harmonized return values from plot functions
  - Added legend position and size arguments to plotSelectionProb()

                       Changes in version 0.99.0                        

  - Preparation for Bioconductor submission

                        Changes in version 0.2.0                        

  - Added a NEWS.md file to track changes to the package.