GSEA v3.0 Release Notes

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GSEA Desktop v3.0 (Jul 2017)


  • This release is open-source on GitHub under a BSD-style license.
  • See Using GSEA v3.0 Features' for a brief introduction and guide.
  • The algorithm in this version of GSEA is unchanged from the former code line and produces results equivalent to the previous version (v2.x).
  • GSEA Desktop v3.0 requires Java 8.

New Features

  • Updated for the MSigDB v6.0 open-access release.
  • The Enrichment Map integration has been updated to work with current versions of Cytoscape (v3.3.0 and newer).
  • Plots and other results can now be saved in the SVG format, which provides improved resolution suitable for publication, better post-analysis editing options, etc. Use the ‘Create SVG plot images’ parameter in the Advanced Fields.
  • MSigDB XML Browser Beta 1 has been released as a separate application to streamline the GSEA Desktop application. See the Downloads page. Another option for investigating genesets is the online MSigDB browser
  • There is a new option for saving the datasets backing the report heatmaps for downstream use & visualization. Use the ‘Create GCT Files’ parameter in the Advanced Fields. These files can be used with e.g. R, GenePattern, Morpheus, or GENE-E among other options.
  • New improvements for long-running file transfer operations include enhanced performance through I/O buffering and compression during transfer, and the addition of a progress bar.
  • Analyses run with a timestamp random seed now record the timestamp value in the HTML Report ‘Other’ section. The same seed can be reused at any time to reproduce the analysis.
  • Implemented a feature to inform the user when a new version is available.

Bug Fixes and Other Improvements

  • Selection of multiple CHIP files for analysis is no longer allowed. This is a simplification that will permit further back-end improvements in the future.
  • Collapse Dataset is no longer allowed with a GSEA Preranked analysis. This was a rarely-used feature that caused a lot of confusion.
  • Fixed an HTML report launcher bug for users with non-English locale settings.
  • Fixed an issue with running the Enrichment Map integration on Mac.
  • Fixed an issue where ‘NaN’ (division by zero) results were given a value of zero in the reports.
  • Fixed issues handling C3 MIR Gene Sets and other gene sets with names containing comma characters.  Set the ‘Alternate Delimiter’ parameter and use a semicolon to separate gene set names.
  • Improved control layout on the lower Tool Command panel.
  • Improved layout of the result chooser panels on the Leading Edge Analysis and Enrichment Map Visualization screens.
  • Updated the Browser Launcher component to fix issues with launching the web browser.
  • Improved the error reporting when there are too few samples in the dataset.
  • Fixed some basic aspects of integration with the Mac OS X menu bar.
  • Removed Thread Controls from the UI as these rarely-used functions led to instability in the application.
  • Improved memory resource use and clean-up during GSEA report generation.
  • Fixed a failure in the Chip Chooser component when not connected to a network.
  • Cleaned up clutter in the application menus and preferences.
  • Better handling for the special internally-used GENE_SYMBOL and SEQ_ACCESSION CHIP files. Please do not use these as inputs to your analyses.
  • In preparation for the open-source release, we made numerous changes toward cleaning up the code base, removing / replacing a number of third-party libraries, and removing unused resources from the GSEA jar file.

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