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Stable release V3.5.0
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@github-actions github-actions released this 08 Feb 22:03
V3.5.0
ce6f731

3.5.0 (2023-02-08)

This version introduces new features such as differential expression analysis with the Limma-Voom pipeline,
customizable databases for the quick-search function, basic filtering and procrssing functions for gene sets,
improved progammatic API for FeatureSet and RankedSet objects, and RPKM and TPM read count normalization.
Several changes have been made to improve the user experience, including updated documentation,
improved clarity of function tooltips, clearer output formats, and faster download speeds for tutorial videos.

Added

  • Added differential expression analysis with the Limma-Voom pipelines (CountFilter.differential_expression_limma_voom)
  • You can now select which databases to display in the right-click quick-search menu, using the settings menu.
  • Gene sets now support some basic operations (filtering, gene ID translating, etc) through the graphical interface.
  • enrichment.FeatureSet and enrichment.RankedSet now support some filtering operations from the filtering module (such as filtering by user-defined attributes, GO terms, or KEGG pathways).
  • Added reads-per-kilobase-million (RPKM) and transcripts-per-million (TPM) normalization methods (CountFilter.normalize_to_rpkm() and CountFilter.normalize_to_tpm()).

Changed

  • Classes enrichment.FeatureSet and enrichment.RankedSet now inherit from Python base-class set, and can be interacted with like other Python sets. The old API and attributes of these classes were maintained as they were.
  • Improved documentation for some functions.
  • Function selection tooltips should now display information more clearly.
  • Pipelines that contain consecutive clustering/splitting functions will now return their outputs in a clearer format.
  • Enrichment bar-plots should now adjust the x-axis limits more tightly to fit the displayed data.
  • Improved clarity of automatic titles in enrichment plots.
  • Download/update speed of tutorial videos has improved significantly.

Fixed

  • Fixed bug where Pipelines would not always properly run 'translate_gene_ids'
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