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Stable release V3.11
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@github-actions github-actions released this 05 Jan 16:47
V3.11
09f4edd

3.11.0 (2024-01-05)

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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