GSEA v4.0.x Release Notes

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GSEA Desktop v4.0.2 (Oct 2019)

• Addition of new collapse modes
• Addition of gene identifier "remap only" mode
• CLI fix for passing individual GMTs vs GP file-list

GSEA Desktop v4.0.1 (Aug 2019)

Miscellaneous bug fixes:

• Fixed an issue with Collapse Dataset that was at-odds with the MSigDB recommendations for symbol remapping.
• Fixed an issue with the Chip Chooser when FTP access is not available.
• Fixed an issue with the Leading Edge Tool when launched from Java Web Start JNLPs.

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 over v3.0 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)