GSEA v3.0 Release Notes

GSEA Home | Downloads | Molecular Signatures Database | Documentation | Contact

GSEA Desktop v3.0 (Jul 2017)

Notes

• 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 www.msigdb.org.
• 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.