Changes in version 1.5.2 - added a warning in runFimo in case bfile argument matches an existing local file. Changes in version 1.4.1 - added an informative error message during importMeme when parse_genomic_coords fails with custom fasta import. Changes in version 1.2.5 - fixed error in ame_compare_heatmap_methods that triggers when plotting without providing a group argument. Changes in version 1.2.4 - updated NAMESPACE to fix R CMD CHECK note. Changes in version 1.2.3 - fixed a bug in importTomTomXML where tomtom list column would contain missing data if tomtom was run using multiple database sources as input. Changes in version 1.2.2 - fixed a bug in runStreme causing failures on data import for STREME version >= 5.4.1 Changes in version 1.2.1 - fixed a bug in runStreme causing failures when using BStringSetLists as input Changes in version 1.1.3 - fixed a bug in runTomTom where setting norc = TRUE failed on data import Changes in version 1.1.1 - runFimo now returns NULL and prints a message when text = FALSE and FIMO detects no matches instead of throwing a cryptic error message Changes in version 0.99.11 - Add support for STREME with runStreme(). STREME will supercede DREME in a future MEME Suite release. Changes in version 0.99.10 - Fixed a bug where paths weren't correctly expanded when used as database entry under certain conditions Changes in version 0.99.8 - Removed inline r call in integrative_analysis vignette to fix issue on bioc build machine Changes in version 0.99.7 - Version bump to force pkg rebuild Changes in version 0.99.6 - added list S3 method for plot_sequence_heatmap so now named lists of sequences can be passed natively to this function. - updated ChIP-seq vignette to demonstrate this Changes in version 0.99.5 - added plot_sequence_heatmap for making heatmaps of sequence lists - Added significantly more explanation to the ChIP-seq vignette - renamed ame_plot_heatmap -> plot_ame_heatmap for consistency Changes in version 0.1.2 - runFimo() skip_matched_sequence default is now FALSE. Set this to TRUE if fimo takes a long time to run, then use add_sequence() to add it back if needed. - runTomTom() dist default is now ed (changed from pearson). Changes in version 0.1.0 - Removed as_universalmotif_df(), as_universalmotif(), and update_motifs(). - These functions are replaced by universalmotif::to_df(), universalmotif::to_list(), and universalmotif::update_motifs() - runDreme and runTomTom results are now returned in universalmotif_df format (behaves just like a data.frame) - The motif column of universalmotif_df objects can no longer be called directly in universalmotif operations like view_motifs(df$motif). Use to_list() for this behavior instead. - To support this change, the pvalue, evalue, and qvalue columns are renamed pval, eval, and qval. The same is true for tomtom output columns match_pvalue -> match_pval, best_match_pvalue -> best_match_pval, etc. - Updated example datasets to use unviversalmotif_df type - ame_plot_heatmap ranking issue is resolved, plots now sort correctly - Added remove_duplicate_motifs and has_duplicate_motifs for detecting and removing duplicated matrices in a universalmotif object or data.frame - Overhauled the Tidying Motifs vignette for more extensive EDA and a demo of deduplication - Updated the flyFactorSurvey_cleaned.meme example database to reflect new changes to the vignette