Rnalysis

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* This version introduces new count matrix normalization methods, as well as MA plots and minor bug fixes.

Added
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* Added the visualization function ma_plot() for CountFilter
* Added functions for the normalization functions Relative Log Ratio (RLE), Trimmed Mean of M-values (TMM), Median of Ratios (MRN), Quantile normalization (quantile)

Changed
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* CountFilter.normalize_to_rpm() was renamed to CountFilter.normalize_to_rpm_htseqcount(), and was supplemented by the more general function for normalizing to Reads Per Million CountFilter.normalize_to_rpm()

Fixed
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* Fixed a bug where some elements of the graphical user interface would not display correctly

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* This version fixes a bug with displaying the tutorial videos in the graphical user interface.

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* This version introduces a graphical user interface for RNAlysis, as well as new functions for KEGG Pathways enrichment analysis.


Added
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* RNAlysis now includes a graphical user interface
* Pipelines can now be imported and exported
* Enrichment and single-set-enrichment for KEGG pathway data

Changed
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* Added function FeatureSet.user_defined_enrichment(), which will replace FeatureSet.enrich_hypergeometric() and FeatureSet.enrich_randomization()
* Updated signature of enrichment.venn_diagram
* enrichment.venn_diagram and enrichment.upset_plot can now be generated on a user-supplied FIgure
* Clustering functions now apply a power transform to count data prior to clustering by default
* Non-deprecated enrichment functions no longer filter the background set by biotype by default
* Changed signature of CountFilter.pca, CountFilter.box_plot, CountFilter.enhanced_box_plot, CountFilter.clustergram, and CountFilter.pairplot to ensure consistency among visualization functions.

Fixed
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* enrichment.venn_diagram can now be plotted with outlines when the circles are unweighted
* Fixed bug in Pipeline.apply_to() where a Filter object would be returned even when the Pipeline was applied inplace

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* This version fixes issues with running GO enrichment that resulted from recent changes to UniProt's API. Moreover, this version slightly improves the performance of some functions.

Changed
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* Fixed issues with running GO enrichment that resulted from changes to UniProt's API.
* Some functions that fetch annotations now cache their results, leading to improved runtimes.
* Updated the documentation of some functions to better reflect their usage and input parameters.

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* This version introduces multiple new features, as well as generally improved graphs and quality-of-life changes.

Added
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* GO enrichment can now generate Ontology Graphs for the statistically significant GO terms.
* Added CountFilter.split_clicom(), an implementation of the CLICOM ensemble-based clustering method (Mimaroglu and Yagci 2012).
* Added Filter.transform(), a method that can transform your data tables with either predefined or user-defined transformations.

Changed
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* CountFilter.pairplot() now uses a logarithmic scale by default.
* Visually improved the graphs generated by many functions, including CountFilter.pairplot() and CountFilter.plot_expression().
* The clusters resulting from all clustering functions are now sorted by size instead of being sorted randomly.

Fixed
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* Minor bug fixes.

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* This version introduces small bug fixes, as well as a new function in the Filtering module.

Added
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* Added Filter.majority_vote_intersection(), which returns a set/string of the features that appear in at least (majority_threhold * 100)% of the given Filter objects/sets.

Changed
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* When mapping/inferring taxon IDs during GO enrichment analysis, organisms will now be prioritized based on their taxon ID values (numerically lower IDs will be considered to be more relevant).

Fixed
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* Fixed bug that occured when mapping/inferring taxon IDs during GO enrichment analysis, where integer taxon IDs would be matched by name similarity before trying an exact ID match, leading to spurious matches.
* Fixed bug that occursed when plotting clustering results with style='all' on Python 3.8.