GSEA v4.1.x Release Notes

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GSEA Desktop v4.1.0 (Jul 2020)

The GSEA v4.1.0 release includes a number of improvements and bug fixes, including:

  • Improved support for macOS Catalina and above, including updates to file choosers and notarization of the Mac application with Apple. This fixes issues with installation and with access to certain user directories considered restricted by Apple (Documents, Desktop, Downloads, network drives, and removable media). The file chooser updates apply to Windows and Linux as well.
  • Updated the Enrichment Report to be more reflective of modern use with RNA-Seq data and newer versions of MSigDB (7.0+).
  • Added the Preranked analysis for annotated reports when Collapse Dataset is used with an annotated CHIP file (in either Collapse or Remap_Only mode).
  • Added a Symbol Mapping Report to the GSEA and Preranked analyses when Collapse Dataset is used (in either Collapse or Remap_Only mode).
  • Added a Purge Selected Files feature to the Recent Files list on the Load Data screen, accessible through the right-click / control-click context menu.
  • Switched all Excel files in the reports to TSV (tab-separated values) files. This addresses an issue with newer versions of Excel complaining about the format and security of the report files: the files previously produced were actually just TSVs with a ".xls" extension, causing Excel to complain about corrupted files.

Miscellaneous bug fixes:

  • Fixed a possible floating-point rounding bug in the mu and sigma adjustment of the standard-deviation calculation used for the Signal2Noise and tTest metrics.
  • Changed the Recent Files list on the Load Data screen to track least-recently-used files for removal when the file limit is reached.
  • Restored the -param_file command-line option, which had been inadvertently removed in the 4.0.0 release.
  • Fixed an issue with the Save Dataset menu option in the Leading Edge report.
  • Fixed an issue with the Exit Handler on macOS.
  • Fixed an issue with the application launcher on certain versions of Windows 10.
  • Minor UI tweaks to cope with HiDPI screens, macOS Dark Mode (note: not supported), screen layout, etc.
  • Numerous points of internal code simplification and modernization, removal of unused code, etc.
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