GSEA v4.0.x Release Notes

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GSEA Desktop v4.0.0 (Aug 2019)


  • The algorithm in this version of GSEA is unchanged from the former code line and produces results equivalent to the previous version (v3.0).
  • GSEA Desktop v4.0.0 requires either Java 11 or Java 8. Java 11 is preferred; we provide bundles with an embedded OpenJDK 11 JVM for Mac, Windows (64-bit), and Linux.

Improvements and Bug Fixes

  • Updated for the MSigDB v7.0 release.
  • Migrated code for Java 11 compatibility and corresponding better security.
  • Performance improvements: we are seeing a roughly 40% improvement in our informal testing.
  • Created dedicated Windows installer,, and Linux bundle, each with an embedded OpenJDK 11 to avoid issues with the user needing to install Java. Created new command-line scripts for launching the GUI and running batch analyses so the user can avoid needing to deal directly with the more complex Java 11 command-line.
  • Removed implicit dependence on out-of-date internal annotation CHIP file.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).
  • 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.
  • Switched from Ant to Gradle for builds.
  • Many code simplifications and removal of unnecessary code.
  • Fixed an indefinite wait cursor in the Leading Edge Tool.

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