Rnalysis

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From this release forward, *RNAlysis* is made available as a stand-alone app for Windows and MacOS. You can download these stand-alone versions from the GitHub Releases page.
In addition, new features were added, including new plots, filtering functions, integration of the external tools bowtie2 and featureCounts, and the ability to generate Gene Ontology Graphs and KEGG Pathway Graphs without running enrichment analysis from scratch.

Added
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* Added a Scree Plot (explained variance per PC) to Principle Component Analysis
* Added CountFilter.split_by_principal_component(), allowing users to filter genes based on their contributions (loadings) to PCA Principal Components.
* Added Filter.drop_columns
* Added support for the Sharpened Cosine distance metric in clustering analyses
* KEGG enrichment can now generate KEGG pathway graphs for pathways that were found to be statistically significant
* Added functions to the enrichment module that can generate KEGG Pathway or Gene Ontology plots based on previously-generated enrichment results
* You can now clear the *RNAlysis* cache from the *RNAlysis* GUI, or through the general module.
* Added bowtie2 alignment to the fastq module.
* Added FeatureCounts feature-counting to the fastq module.
* You can now choose whether or not to discard genes from enrichment analysis if they have no annotations associated with them.
* When right-clicking on a specific cell in a table or line in a gene set view, a context menu will open, allowing you to copy the associated value, or look it up in one of few common biology databases.
* Added sections to the programmatic user guide about the `fastq` module.

Changed
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* Replaced the 'parallel' parameter in enrichment functions with the 'parallel_backend' parameter, allowing users to choose which parallel backend (if any) will be used in the function.
* Added 'parallel_backend' parameter to all clustering functions under the filtering module.
* When generating Gene Ontology/KEGG Pathway graphs, users can choose whether or not to generate the figure in an additional separate file.
* Updated type annotations of some functions to be more precise and helpful (for example, setting a lower bound on some int function parameters).
* The colorbar ticks in enrichment bar plots now match the axis ticks on the main axis.
* Slight improvements in GUI performance, stability, and looks.
* Slight improvements in performance of enrichment analysis when examining a small number of attributes.
* enrichment.plot_enrichment() was replaced by enrichment.enrichment_bar_plot().
* CountFilter.differential_expression() has new optional parameter `output_folder`, which allows users to save the generated data tables and the R script that generated them into a specified folder.

Fixed
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* In CountFilter.differential_expression_deseq2(), fixed a bug where design matrix files with non-comma delimiters would cause an error (thanks to `Mintxoklet <https://github.com/Mintxoklet>`_ in `#7 <https://github.com/GuyTeichman/RNAlysis/issues/7>`_)
* Fixed bug where setup.py would install a directory named tests into site-packages folder (thanks to `Bipin Kumar <https://github.com/kbipinkumar>`_ in `#9 <https://github.com/GuyTeichman/RNAlysis/issues/9>`_)
* Fixed bug where the windows of some functions (differential expression, adapter trimming, etc) did not show a link to the function's documentation page.
* Fixed typos in some parts of the *RNAlysis* documentation
* When filtering a table by a single user-defined attribute, the automatic table name will now be more informative about the operation applied.
* Fixed bug where occasionally a Pipeline or Function would generate multiple tables of the same name, but only one of them will appear in the GUI.
* Fixed bug where occasionally significance asterisks on enrichment bar-plots would appear in the wrong location.
* Fixed bug where fastq.create_kallisto_index() (Create Kallisto Index) would not make use of the `make_unique` parameter (thanks to Matthias Wilm)

Removed
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* Removed the previously-deprecated functions `enrichment.enrich_randomization()` and `enrichment.enrich_hypergeometric()`.



New Contributors
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* `Mintxoklet`_ in `7`_
* `Bipin Kumar`_ in `9`_
* Matthias Wilm

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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