GSEA v4.0.x Release Notes

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* Changed the Cytoscape integration to avoid issues with platform-specific launching issues, newer Cytoscape versions, multiple installations, custom installations, and so on.  The integration now prompts the user to launch Cytoscape manually before it attempts to connect.  Cytoscape 3.3+ is required.
* Changed the Cytoscape integration to avoid issues with platform-specific launching issues, newer Cytoscape versions, multiple installations, custom installations, and so on.  The integration now prompts the user to launch Cytoscape manually before it attempts to connect.  Cytoscape 3.3+ is required.
* Fixed an indefinite wait cursor in the Leading Edge Tool.
* Fixed an indefinite wait cursor in the Leading Edge Tool.
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* DAVID I WANT TO REMOVE THIS ONE. UNLESS THERE ARE ANY USER-FACING IMPLICATIONS OF THIS CHANGE? IN WHICH CASE CAN THEY BE DESCRIBED INSTEAD? Removed implicit dependence on out-of-date internal annotation CHIP file.  Removed other special CHIP handling code to avoid conflicting with the results of the new symbol conversion from MSigDB 7.0 and better support RNA-Seq workflows.  Annotations now come from the CHIP used to collapse, or else from the dataset itself (and are left untouched).
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* Updated the annotations and processing code used by the GSEA application to match the new symbol conversion procedure used to create MSigDB 7.0 (see the [https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/MSigDB_v7.0_Release_Notes MSigDB release notes])

Revision as of 04:39, 20 August 2019

61GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact


GSEA Desktop v4.0.0 (Aug 2019)

The GSEA v4.0.0 release includes a number of improvements and bug fixes, including:

  • Updates for the MSigDB v7.0 release.
  • Updates for compatibility with Java 11 and the (free) OpenJDK version of Java.
  • New options for downloading and launching the application:
    • Windows installer, Mac app, and Linux bundle, each with an embedded OpenJDK Java 11, which means no separate Java installation is needed.
    • Command-line scripts for running batch analyses, which means users no longer need to enter Java commands directly. Note that a separate Java 11 installation is required.
    • Note: Launching the application using Java Web Start still requires a separate Java 8 installation.
  • Miscellaneous performance improvements and code simplifications. These add up to a roughly 40% improvement in our informal testing.
  • Changed the Cytoscape integration to avoid issues with platform-specific launching issues, newer Cytoscape versions, multiple installations, custom installations, and so on. The integration now prompts the user to launch Cytoscape manually before it attempts to connect. Cytoscape 3.3+ is required.
  • Fixed an indefinite wait cursor in the Leading Edge Tool.
  • Updated the annotations and processing code used by the GSEA application to match the new symbol conversion procedure used to create MSigDB 7.0 (see the MSigDB release notes)
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