GSEA v4.0.x Release Notes

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GSEA Desktop v4.0.3 (Nov 2019)

Miscellaneous bug fixes:

• Fixed CHIP parsing bugs related to empty values, whitespace, null, etc.
• Fixed a command-line option bug so the "-collapse" parameter is not required.
• Changed GSEA cache browsers to sort by date.
• Changed tab order for GMT chooser

GSEA Desktop v4.0.2 (Oct 2019)

• Addition of new Mean_of probes and Sum_of_probes collapse modes.
• Addition of gene identifier "Remap_Only" operation, to map datasets with older symbols to MSigDB's canonical namespace (Ensembl 97 in MSigDB 7.0). See the MSigDB release notes for a discussion of recent changes to MSigDB symbol mapping procedures and our corresponding new recommendations for data set handling.
  • Note that the UI around the Collapse function has changed to accommodate this new operation. The former true/false "Collapse dataset to gene symbols" parameter has been changed to "Collapse/Remap to gene symbols", with options "Collapse / No_Collapse / Remap_Only".
  • The various collapse modes are ignored when remapping, and GSEA will report an error if the dataset contains multiple input symbols that map to the same gene in the specified CHIP file. Remap_Only is intended as a symbol conversion step and nothing more.
  • The command-line parameters dealing with the Collapse function remain the same as before but now take these new option values; use the GUI "Command" function to view examples of usage. As a convenience, GSEA will continue to accept "true" and "false" as aliases for "Collapse" and "No_Collapse", respectively.
• Restoration of the Collapse function to GSEA Preranked.
  • This was removed in the past because the GSEA team could not vouch for the use of any particular collapse mode when dealing with unknown custom user-defined ranking metrics. We have restored it with a default of Remap_Only primarily to support the need to update old datasets to Ensembl 97.
  • Use the other collapse modes with custom ranking metrics at your own discretion. We recommend you consult with a local statistician to make sure any such collapsing steps are valid for your chosen metric, or handling such steps upstream before applying any metric.
• Command-line fix for passing individual GMTs vs a GenePattern file-list. Use the -gmx option to pass a single file and the new -gmx_file option to pass a GP style list of multiple files.

Again, use the GUI "Command" function to view examples of usage.

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)