Changes in version 1.13.1                        

  - Fixed an error in importAme that prevented import when runAme was
    run with sequences = TRUE (Reported by @withermatt on Github. Thank
    you!)

                        Changes in version 1.7.1                        

  - Fixed typos describing the parse_genomic_coord parameter in runFimo
    and runMeme documentation & error messages for clarity. (Nice catch,
    Soren Heidelbach!)
  - Added CITATION file

                        Changes in version 1.7.0                        

  - Fixed a bug in parseStreme causing motif ids and list object names
    to be out of sync.
  - Changed parseStreme and runStreme output motif ids slightly to
    always pad leading 0's to the numeric ids, consistent with how other
    MEME Suite tools behave. For instance, a previous motif may be named
    "m1-ATGC", will now be named "m01-ATGC". This may cause slight code
    breakage if filtering on specific hard-coded ids. This change also
    ensures correct sorting order of motif outputs consistent with the
    behavior of the rest of the package.

                        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