NEWS.md

In snystrom/dremeR: motif matching, comparison, and de novo discovery using the MEME Suite

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

snystrom/dremeR documentation built on Sept. 26, 2024, 6:41 p.m.