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.