NEWS

memes 1.19.1

Removes ggseqlogo dependency as it is being archived from CRAN, standardizes on universalmotif::view_logo for any internals that did not already use it (thanks @bjmt for the implementation hint)
@karawoo fixed a CI bug

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

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

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.

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

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

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

fixed a bug in importTomTomXML where tomtom list column would contain missing data if tomtom was run using multiple database sources as input.

fixed a bug in runStreme causing failures on data import for STREME version >= 5.4.1

runFimo now returns NULL and prints a message when text = FALSE and FIMO detects no matches instead of throwing a cryptic error message

Add support for STREME with runStreme(). STREME will supercede DREME in a future MEME Suite release.

Fixed a bug where paths weren't correctly expanded when used as database entry under certain conditions

Removed inline r call in integrative_analysis vignette to fix issue on bioc build machine

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

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).

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