# 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
