Changelog

Source: NEWS.md

monaLisa 1.9.1

  • adapt dumpJaspar to also work with JASPAR2024

monaLisa 1.7.1

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

monaLisa 1.3.1

  • update citation information

monaLisa 1.1.2

  • added citation to the Bioinformatics publication

monaLisa 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.

monaLisa 1.0.0

  • Initial release of monaLisa as part of Bioconductor 3.14

monaLisa 0.99.5

  • Updated R/monaLisa-package.R file

monaLisa 0.99.4

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

monaLisa 0.99.3

  • Updated README.md file

monaLisa 0.99.2

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

monaLisa 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()

monaLisa 0.99.0

  • Preparation for Bioconductor submission

monaLisa 0.2.0

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