Rnalysis

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This release brings several exciting new features.
Notably, these inclue the ability to run functions from the Picardtools suite, and the ability to automatically save interactive session reports and later resume them from any saved session.
In addition, this release includes several visual upgrades, bug fixes, and quality-of-life improvements.
Happy analysis!

Added
*******
* *RNAlysis* can now run functions from the Picardtools suite, including conversion functions (BAM to SAM, SAM to FASTQ, FASTQ to SAM, etc), quality control (validate SAM), and post-processing functions (remove PCR duplicates, sort SAM, create BAM index).
* *RNAlysis* interactive session reports can now be resumed from any saved session, instead of having to start a new report from scratch. When loading a session created by *RNAlysis* 3.11 and beyond, you will have the option to resume the interactive report from the last saved state.

Changed
********
* CutAdapt adapter trimming functions can now receive an optional "new_filenames" parameter, which allows users to specify the names of the output files.
* Hierarchical clustergram plot (CountFilter.clustergram) now supports the 'colormap' parameter, which allows users to specify a custom color map for the plot.
* Hierarchical clustergram plot (CountFilter.clustergram) now displays continuous values on the color bar, instead of discrete values.
* Generally improved the looks of Hierarchical clustergram plot (CountFilter.clustergram).
* Previously-added functions (such as ortholog/paralog mapping, biotype summary by GTF file, etc) can now be applied to gene sets. Previously, some of these functions could only be applied to data tables.

Fixed
*******
* Function "Summarize feature biotypes (based on a reference table)" (biotypes_from_ref_table) now treats rows with missing values as "_missing_from_biotype_reference" instead of ignoring them entirely.
* Fixed bug where the Ensembl paralog-finding function would appear under the wrong tab in the graphical interface.
* Fixed bug where the description of the MA Plot function and parameters would not display correctly in the graphical interface.

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Version 3.10.1 introduces several bug fixes, as well as well as support for random effect analysis in Limma-Voom differential expression.

Added
*******
* Limma-Voom differential expression can now fit mixed linear models containing a random effect (e.g. nested design).


Fixed
*******
* Fixed bug where trying to load sessions created with RNAlysis version 3.10.0 would result in an error.
* Fixed bug where using the OrthoInspector ortholog mapping function with database='auto' would sometimes fail to find an appropriate mapping database, even when one exists.
* Fixed bug where kallisto paired-end quantification window would display the 'read1' and 'read2' parameters twice.
* Fixed bug where empty sub-menus would appear under the FASTQ menu. These sub-menus will be implemented in future versions of RNAlysis.

-------------------
I'm thrilled to introduce RNAlysis version 3.10.0.
This version includes features that were requested by users for a while, alongside quality-of-life improvements and bug fixes.
Here is a brief highlight of the most important additions:

**Ortholog Mapping:** *RNAlysis* can now map genes to their closest orthologs in different organisms.
You can map genes to their orthologs using four different databases - Ensembl, Panther, PhylomeDB, and OrthoInspector - extracting both one-to-one and one-to-many ortholog relationships and filtering them based on their reliability.

**Discovering Paralogs:** In the same vein, *RNAlysis* now facilitates the discovery of paralogs within a specific organism, using either the Ensembl or Panther databases.

**New visualization and analysis options for Principal Component Analysis (PCA):** We've introduced new functions and parameters to allow you to get more out of your principal component analysis.

I would also like to extend my personal apology for the delay in bringing you this update.
Due to personal reasons, this release, originally scheduled for the end of August, took longer than expected.
Your patience and support have been invaluable, and I'm eager to share these exciting additions with you.
Thank you for being a part of the RNAlysis community, and stay tuned for more updates in the near future!

Added
*******
* Added new functions to the filtering module that map genes to their closest orthologs in a different organism, using four different databases: Ensembl, Panther, PhylomeDB, and OrthoInspector.
* Added new functions to the filtering module that find paralogs of genes in a given organism, using two different databases: Ensembl and Panther.
* Added new function 'Sort table by contribution to a Principal Component (PCA)' (CountFilter.sort_by_principal_component), which allows sorting of genes in a count matrix by their contribution (gene loadings) to a principal component.
* Added a new parameter called 'legend' to 'Principal Component Analysis (PCA) plot' (CountFilter.pca), which allows users to display a legend on the PCA plot with a name for each sample group/color.

Changed
********
* RNAlysis now issues a warning when users run PCA or PCA-based functions on an unnormalized count matrix.
* The 'seek_fusion_genes' and 'learn_bias' arguments for kallisto quantification (fastq.kallisto_quant_single_end and fastq.kallisto_quant_paired_end), which were depracated in kallisto versions >0.48, are no longer displayed on the graphical interface. Old Pipelines that contain these arguments will still run, but new Pipelines will not contain them.
* Long-running functions now run in the background even when the 'inplace' parameter is set to True, instead of freezing the entire graphical interface.

Fixed
*******
* Fixed bug where functions would sometimes fail to run without displaying an error message.
* Fixed bug where progress bars in the graphical interface would sometimes not disappear after reaching 100% completion.
* RNAlysis should no longer display warning messages about graph layout when graphs are scaled down.
* Fixed bug where the clustergram function (CountFilter.clustergram) would raise an error with specific sets of dependecy versions.
* Loading tables no longer raises a depracation warning when using newer versions of Pandas.

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This patch contains bug fixes and improved functionality for enrichment lollipop plots,
as well as bug fixes for issues with the stand-alone version.

Changed
********
* Single-set enrichment result tables now contain observed/expected values based on the XL-mHG test cutoff.
* When loading a differential expression design matrix, RNAlysis now issues an error if the design matrix column names contain invalid characters.
* Updated the scaling of enrichment lollipop plots to make small 'observed' values easier to discern.

Fixed
*******
* Fixed bug where an error message would sometimes appear after RNAlysis finishes generating an automatic session report on the stand-alone app.
* Fixed bug where enrichment lollipop plots in horizontal mode would display the observed/expected values in reverse order.
* Fixed bug where enrichment lollipop plots and the 'show_exp' parameter would not work on single-set enrichment data.
* Fixed bug where sometimes the tab label of clustering/differential expression output tables would not match the name of the generated table.

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Version 3.9.1 of RNAlysis introduces several improvements and fixes to further improve your analysis experience.
The release includes new optional parameters for single-set enrichment functions, compatibility improvements with newer Python versions,
improved error messaging for R scripts, and adresses minor issues related to enrichment analysis, documentation, plotting parameters, and Pipeline saving.

Added
*******
* Added new optional parameters to single-set enrichment functions, allowing users to determine the top and bottom cutoffs for the XL-mHG test ("X" and "L").

Changed
********
* RNAlysis single-set enrichment analysis using the XL-mHG test now supports Python versions >= 3.8.
* RNAlysis stand-alone app is now built on Python 3.11, improving overall performance.
* Error messages caused by running R tools such as DESeq2, Limma-Voom, and FeatureCounts will now clearly state the reason the script failed, making it easier to understand what went wrong.

Fixed
*******
* Fixed bug where enrichment analysis would raise an error when running enrichment analysis on a gene set with no relevant annotations, or a gene set that does not intersect at all with the background gene set.
* Added missing documentation for plotting parameters in some enrichment functions.
* Depracation Warning should no longer appear when generating a box-plot or enhanced box-plot with scatter=True (CountFilter.box_plot, CountFilter.enhanced_box_plot)
* Fixed bug in featureCounts single-end mode where the 'output_folder' parameter could appear as disabled.
* Fixed bug where RNAlysis would raise an error message after saving a Pipeline, even when the Pipeline was saved successfully.

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Version 3.9.0 of *RNAlysis* introduces several enhancements and fixes to improve your experience.
The release includes additional enrichment plot styles, a new option for PCA plots,
the ability to load and save data tables in Parquet format, and new actions in the Help menu for reporting issues and suggesting improvements.
The update also improves the performance of various functions, ensures consistency in font and theme settings,
and addresses multiple bug fixes, including issues with automatic session reports and visualization functions.

Added
*******
* Added additional parameters to enrichment bar plots (enrichment.enrichment_bar_plot), including a new plot style ('lollipop') and observed/expected labels on the graph.
* Added a new parameter to Principal Component Analysis plots (CountFilter.pca) 'plot_grid', which can enable or disable adding a grid to PCA plots.
* RNAlysis can now load and save data tables in Parquet format (.parquet)
* Added new actions to the Help menu, allowing users to report issues, suggest issues, or open discussions.

Changed
********
* Functions in the FASTQ model are now added to automatic session reports.
* Many of the functions in RNAlysis should now run faster.
* Font type, size, and color for help tooltips should now match the global font settings.
* True/False toggle switches now scale with font size.
* When loading data tables into RNAlysis, you will now see only supported file formats by default.
* Clustering PCA plots are now plotted in proportion to the % variance explained by each PC.
* The legend in clustering PCA plots is now draggable.

Fixed
*******
* Fixed bug where data tables generated through the FASTQ model would not display properly in automatic session reports.
* Fixed bug where graphs generated through the Visualize Gene Sets window would not be added to automatic analysis report.
* When saving a file through the graphical interface, automatically-suggested filenames no longer contain illegal characters.
* Improved clarity of error message when R installation folder is not found.
* Fixed bug where some input parameter widgets in the RNAlysis graphical interface would not display properly.
* RNAlysis now provides a clearer warning message when attempting to run HDBSCAN clustering, if the hdbscan package is not installed.
* Label text in PCA plots and hierarchical clustergrams should no longer be cropped outside of the visible region of the plot.
* Fixed bug where some visualization functions, such as pair-plot (CountFilter.pairplot) would not display properly due to version mismatches between pandas and seaborn.
* Improved clarity of error messages when external apps' (kallisto, bowtie2, etc) installation folders are not found.
* Fixed bug where running the RNAlysis graphical interface on a new computer would sometimes raise an error (thanks to `NeuroRookie <https://github.com/NeuroRookie>`_ in `#25 <https://github.com/GuyTeichman/RNAlysis/issues/25>`_).
* Fixed a bug where the 'min_samples' parameter in HDBSCAN clustering could not be disabled.
* Fixed a bug where applying a function to a gene set with inplace=False would cause the new gene set to be called 'New Table'.
* Fixed a bug where RNAlysis would display the message "Pipeline saved successfully", even when the user cancels the save operation.

New Contributors
*****************
* `NeuroRookie`_ in `25`_