Changelog

Source: NEWS.md

memes 1.2.2

  • fixed a bug in runStreme causing failures on data import for STREME version >= 5.4.1 # memes 1.2.1
  • fixed a bug in runStreme causing failures when using BStringSetLists as input # memes 1.1.3
  • fixed a bug in runTomTom where setting norc = TRUE failed on data import # memes 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 # memes 0.99.11
  • Add support for STREME with runStreme(). STREME will supercede DREME in a future MEME Suite release. # memes 0.99.10
  • Fixed a bug where paths weren’t correctly expanded when used as database entry under certain conditions # memes 0.99.8
  • Removed inline r call in integrative_analysis vignette to fix issue on bioc build machine # memes 0.99.7
  • Version bump to force pkg rebuild # memes 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

memes 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

memes 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).

memes 0.1.0

  • Removed as_universalmotif_df(), as_universalmotif(), and 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