GSEA v4.0.x Release Notes
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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)