Rnalysis

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* This version introduced quality-of-life improvements to the graphical user interface.

Added
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* Added a Frequently Asked Questions page, and linked all *RNAlysis* help material inside the graphical interface Help menu.
* Pipelines can now be edited and deleted through the Pipeline menu of the graphical interface.
* Added Contributing page to the documentation, with basic guidelines on how you can contribute to the *RNAlysis* project!

Changed
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* All open tabs are now always visible in the main menu screen. Tab names are now shortened with ellipsis if nessecary.
* The right-click context menu of the main menu tabs now allows users to open a new tab at a specific position, or close a specific tab/tabs to the right/tabs to the left/all other tabs.
* *RNAlysis* documentation is now split into GUI documentation (quick-start video guide, tutorial, GUI user guide), and programmatic documentation (programmatic user guide)
* Improved readability of *RNAlysis* logs
* Pipelines are now exported with additional metadata - the version of *RNAlysis* they were exported from, and the date and time it was exported. This metadata should not affect Pipelines that were created in older versions, and does not affect the way Pipelines are applied to data tables.

Fixed
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* *RNAlysis* now warns users if they attempt to overwrite an existing Pipeline.
* Fixed an incorrect keyboard shortcut for Export Pipeline action

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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.