Rnalysis

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Fixed
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* Fixed bug with DESeq2 automatic installation on Windows computers.

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Changed
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* Updated citation information for *RNAlysis*

Fixed
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* Fixed typos in the *RNAlysis* tutorial

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* This version introduces quality-of-life changes to the graphical user interface, functions for translating gene IDs and running differential expression analysis, and extends RNAlysis to support Python versions 3.9 and 3.10.

Added
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* Added Filter.translate_gene_ids()
* Added CountFilter.differential_expression_deseq2()
* Added Filter.filter_by_kegg_annotations()
* Added Filter.filter_by_go_annotations()
* Added CountFilter.average_replicate_samples()
* Added fastq module that contains adapter-trimming functions utilizing CutAdapt, and mRNA-sequencing quantification using kallisto.

Changed
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* Added additional plotting parameters to visualization functions.
* Improved performance of some aspects of the graphical user interface.
* RNAlysis' basic features are now supported on Python versions 3.9 and 3.10.
* CountFilter.pca() now generates a plot for *every* pair of Principal Components requested by the user.
* CountFilter.split_clicom() now supports clustering each batch of replicates separately, using the 'replicates_grouping' parameter
* Biotype-based filtering and summary can now be done based on GTF annotation files instead of a Biotype Reference Table.
* Filter.biotypes() was refactored into Filter.biotypes_from_ref_table()
* Filter.filter_biotype() was refactored into Filter.filter_biotype_from_ref_table()

Fixed
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* Users can now queue multiple computationally-intense enrichment/clustering tasks while another task is running.
* Fixed a bug where sometimes some function parameters would disappear from the graphical user interface.
* Fixed a bug where exceptions during computationally-intense tasks would cause *RNAlysis* to crash.
* Auxillary windows are now properly minimized when analysis starts, and restored when analysis ends or encounters an error.

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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