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@github-actions github-actions released this 06 May 20:10
V3.8.0
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3.8.0 (2023-05-07)

Version 3.8.0 of RNAlysis comes with several exciting new features, including the ability to generate interactive analysis reports automatically.
This feature allows users to create an interactive graph of all the datasets they loaded into RNAlysis, the functions applied, and the outputs generated during the analysis.
You can read more about this feature in the Tutorial chapter and the User Guide chapter.

The new release also includes Pipelines for FASTQ functions, the ability to export normalization scaling factors, and other changes to improve the software's performance.
RNAlysis now supports Python 3.11, and many functions should now run faster. The software's graphic interface has also improved significantly, and users will now see a clearer error message when attempting to load unsupported file formats.
Lastly, the release also fixes several bugs.

Please note that, since Python 3.7 will be reaching end of life as of June 2023, new versions of RNAlysis will no longer support it.

Added

  • You can now generate interactive analysis reports automatically using the RNAlysis graphical interface. Read more about this feature here.
  • Added Pipelines for the FASTQ module (SingleEndPipeline and PairedEndPipeline), allowing you to apply a series of functions (adapter trimming, alignment, quantification, etc) to a batch of sequence/alignment files.
  • Added new parameter 'return_scaling_factors' to normalization functions, that allows you to access the scaling factors calculated by RNAlysis.
  • Added new parameter 'gzip_output' to CutAdapt adapter trimming (fastq.trim_adapters_single_end and fastq.trim_adapters_paired_end), allowing users to determine whether or not the output files will be gzipped.

Changed

  • RNAlysis now supports Python 3.11, and no longer supports Python 3.7.
  • Many of the functions in RNAlysis should now run faster.
  • The RNAlysis graphic interface should now boot up significantly faster.
  • RNAlysis now shows an easier to understand error message when users attempt to load a table in an unsupported format (e.g. Excel files).
  • CutAdapt adapter trimming (fastq.trim_adapters_single_end and fastq.trim_adapters_paired_end) now outputs non-gzipped files by default.
  • Standardized all plotting functions in the filtering module to return a matplotlib Figure object, which can be further modified by users.

Fixed

  • RNAlysis failing to map gene IDs during GO enrichment analysis should no longer raise an error (thanks to clockgene in #16).
  • Fixed bug where the Command History window would not display history of the current tab immediately after clearing the current session.
  • Fixed bug where adapter trimming would fail to run when using CutAdapt version >= 4.4.0.
  • Fixed bug where 'Filter rows with duplicate names/IDs' (Filter.filter_duplicate_ids) would raise an error when applied to some tables.

New Contributors

  • [clockgene] in [#16]
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