Software v2 release notes

Software updates: v2 of the GSEA java desktop application has been released.

What's new in GSEA Java v2.0

Thanks to feedback from several users over the past year we have made changes to improve the usability of the software. We have also added a few new features. The algorithm has not changed. The main new features and enhancements in GSEA java v2.0 include:

1. Leading Edge Analysis

Implementation of this


2. Documentation



3. Integrated Gene Sets Browser

4. Many more gene sets along with annotations in the form of Gene Set Cards

5. Chip2Chip

6. Usability enhancements to the Java Graphical User Interface

• A seperate tool is provided which can run GSEA on preranked gene lists
• Heat maps can be generated in headless mode
• Improved performance with very large gene set databases
• A memory monitor displays how much memory is being used / available. Clicking the icon by its side runs the garbage collector in an attempt to free up memory.
• Added to phenotype chooser parameter is the ability to use the expression profile of a gene in the dataset as a phenotype (continuous vector) for gsea (refer to the Pegtel paper).
• Context sensitive help- these are special help buttons distributed throughtout the java GUI. On user click they open up a URL at the GSEA doc website.
• Default output folder can be anywhere now. Use the preferences to change the path.
• New edb folder made with GSEA results that are a machine parsable version of enrichment results
• Application messages can be viewed in the status bar at the bottom of the interface.