GSEA v4.0.x Release Notes

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<h2> GSEA Desktop v4.0.2 (Oct 2019)</h2>
<h2> GSEA Desktop v4.0.2 (Oct 2019)</h2>
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* Addition of new collapse modes
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* Addition of new Mean_of probes and Sum_of_probes collapse modes.
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* Addition of gene identifier "remap only" mode
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* Addition of gene identifier "remap only" mode.  See the [https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/MSigDB_v7.0_Release_Notes#Changes_to_MSigDB_Gene_Symbol_Mapping_Procedures MSigDB release notes] for a discussion of recent changes to MSigDB symbol mapping procedures and our corresponding [https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/MSigDB_v7.0_Release_Notes#Changes_to_data_set_handling_recommendations new recommendations for data set handling].
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* CLI fix for passing individual GMTs vs GP file-list
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* CLI fix for passing individual GMTs vs GP file-list.
<h2> GSEA Desktop v4.0.1 (Aug 2019)</h2>
<h2> GSEA Desktop v4.0.1 (Aug 2019)</h2>

Revision as of 04:51, 25 October 2019

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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" mode. 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.
  • 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)
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