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NEWS.md

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memes 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!)

memes 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

memes 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.

memes 1.5.2

  • added a warning in runFimo in case bfile argument matches an existing local file.

memes 1.4.1

  • added an informative error message during importMeme when parse_genomic_coords fails with custom fasta import.

memes 1.2.5

  • fixed error in ame_compare_heatmap_methods that triggers when plotting without providing a group argument.

memes 1.2.4

  • updated NAMESPACE to fix R CMD CHECK note.

memes 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.

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().
    • 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