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Stable release V3.7.0
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@github-actions github-actions released this 07 Apr 11:01
V3.7.0
b8635eb

3.7.0 (2023-04-07)

This version introduces small RNA read alignment using ShortStack, new filtering functions, a new optional parameter for Principal Component Analysis, improvements to the graphical interface, and bug fixes.

Added

  • Added small RNA read alignment using ShortStack (fastq.shortstack_align_smallrna).
  • Added new filtering function 'Filter specific rows by name' (Filter.filter_by_row_name).
  • Added new filtering function 'Filter rows with duplicate names/IDs' (Filter.filter_duplicate_ids).
  • Function parameters in pop-up windows in the graphical interface can now be imported and exported.
  • Added new parameter to Principal Component Analysis (CountFilter.pca) 'proportional_axes', that allows you to make the PCA projection axes proportional to the percentage of variance each PC explains.
  • Improved clarity of error messages in the graphical interface.

Changed

  • Tables loaded into RNAlysis that use integer-indices will now be converted to use string-indices.
  • Refactored CountFilter.from_folder into CountFilter.from_folder_htseqcount, and added a new CountFilter.from_folder method that accepts a folder of count files in any format.
  • In the RNAlysis graphical interface, optional parameters that can be disabled will now display the hint "disable this parammeter?" instead of "disable input?".
  • Added optional parameter 'ylim' to 'create enrichment bar-plot' function (enrichment.enrichment_bar_plot), allowing users to determine the Y-axis limits of the bar plot.
  • Updated function signatures of 'Visualize gene ontology' and 'Visualize KEGG pathway' (enrichment.gene_ontology_graph and enrichment.kegg_pathway_graph) to make more sense.
  • Removed parameter 'report_read_assignment_path' from featureCounts feature counting (fastq.featurecounts_single_end and fastq.featurecounts_paired_end).
  • The RNAlysis graphical interface should now load more quickly.
  • Progress bars in the graphical interface should now reflect elapsed/remaining time for tasks more accurately.

Fixed

  • Fixed bug in the function 'Split into Higly and Lowly expressed genes' (Filter.split_by_reads) where the two resulting tables would be named incorrectly (highly-expressed genes would be labeled 'belowXreads' and vice-versa).
  • Fixed bug where the 'column' parameter of some functions ('Filter by percentile', 'Split by percentile', 'Filter with a number filter', 'Filter with a text filter') would not automatically detect column names in the graphical interface.
  • Fixed bug where the 'numerator' and 'denominator' parameters of of the function 'Calculate fold change' would not automatically detect column names in the graphical interface.
  • Fixed bug where tables with integer-indices could not be visualized properly through the graphical interface.
  • Fixed bug in the function 'featureCounts single-end' (fastq.featurecounts_single_end) where setting parameter 'report_read_assignment' to any value other than None would raise an error.
  • Functions that take column name/names as input (transform, filter_missing_values, filter_percentile, split_percentile) can now be applied to fold change tables (FoldCangeFilter objects).
  • Fixed bug where the description for the 'n_bars' parameter of the 'create enrichment bar-plot' function (enrichment.enrichment_bar_plot) would not display properly.
  • 'Visualize gene ontology' and 'Visualize KEGG pathway' (enrichment.gene_ontology_graph and enrichment.kegg_pathway_graph) now have proper parameter descriptions.
  • Fixed bug where in-place intersection and difference in the filtering module would fail when using recent versions of pandas.
  • Fixed bug where graphs generated through the Visualize Gene Sets window would not immediately display when using the RNAlysis stand-alone app.
Assets 4
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