NEWS

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monaLisa 1.17.1

• clarifications of supported families for the stability selection

monaLisa 1.15.3

• minor updates to adjust to breaking changes in ggplot2 version 4

monaLisa 1.15.2

• minor updates to adjust to functionality migrated from GenomeInfoDb to new Seqinfo package

monaLisa 1.13.3

• switched to ggplot2 with all plotting functions (except plotMotifHeatmaps that is still based on ComplexHeatmaps)
• new arguments introduced in plotStabilityPaths() to allow for labels to be shown at the end of the stability paths if desired
• changed some argument names in plotStabilityPaths() and plotStabilityPaths(). See the help pages of these function for more details
• updated the stability selection vignette to showcase labeling predictors
• exposed glmnet arguments in randLassoStabSel()

monaLisa 1.13.2

• minor fix to ensure that heatmap bin legends are ordered in the same way as the heatmap columns

monaLisa 1.11.3

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

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.