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.