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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
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* 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
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* 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
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* 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.