Difference between revisions of "GSEA v4.0.x Release Notes"

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<h2> GSEA Desktop v4.0.3 (Nov 2019)</h2>
 +
Miscellaneous bug fixes:
 +
* Fixed CHIP parsing bugs related to empty values, whitespace, null, etc.
 +
* Fixed a command-line option bug so the "-collapse" parameter is not required.
 +
* Changed GSEA cache browsers to sort by date.
 +
* Changed tab order for GMT chooser
 +
 +
<h2> GSEA Desktop v4.0.2 (Oct 2019)</h2>
 +
* Addition of new Mean_of probes and Sum_of_probes collapse modes.
 +
* Addition of gene identifier "Remap_Only" operation, to map datasets with older symbols to MSigDB's canonical namespace (Ensembl 97 in MSigDB 7.0).  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].
 +
** Note that the UI around the Collapse function has changed to accommodate this new operation.  The former true/false "Collapse dataset to gene symbols" parameter has been changed to "Collapse/Remap to gene symbols", with options "Collapse / No_Collapse / Remap_Only".
 +
** The various collapse modes are ignored when remapping, and GSEA will report an error if the dataset contains multiple input symbols that map to the same gene in the specified CHIP file.  Remap_Only is intended as a symbol conversion step and nothing more.
 +
** The command-line parameters dealing with the Collapse function remain the same as before but now take these new option values; use the GUI "Command" function to view examples of usage.  '''As a convenience, GSEA will continue to accept "true" and "false" as aliases for "Collapse" and "No_Collapse", respectively'''.
 +
* Restoration of the Collapse function to GSEA Preranked.
 +
** This was removed in the past because the GSEA team could not vouch for the use of any particular collapse mode when dealing with unknown custom user-defined ranking metrics.  We have restored it with a default of Remap_Only primarily to support the need to update old datasets to Ensembl 97.
 +
** '''Use the other collapse modes with custom ranking metrics at your own discretion.'''  We recommend you consult with a local statistician to make sure any such collapsing steps are valid for your chosen metric, or handling such steps upstream before applying any metric.
 +
* Command-line fix for passing individual GMTs vs a GenePattern file-list.  Use the '''-gmx''' option to pass a single file and the new '''-gmx_file''' option to pass a GP style list of multiple files.
 +
Again, use the GUI "Command" function to view examples of usage.
 +
 +
<h2> GSEA Desktop v4.0.1 (Aug 2019)</h2>
 +
 +
Miscellaneous bug fixes:
 +
 +
* Fixed an issue with Collapse Dataset that was at-odds with the [https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/MSigDB_v7.0_Release_Notes 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.
 +
 
<h2> GSEA Desktop v4.0.0 (Aug 2019)</h2>
 
<h2> GSEA Desktop v4.0.0 (Aug 2019)</h2>
−
<p>
+
 
−
<h3>Notes</h3>
+
The GSEA v4.0.0 release includes a number of improvements and bug fixes, including:
−
  <ul style="margin-top:0pt;margin-bottom:0pt;">
+
 
−
    <li dir="ltr" style="list-style-type:disc>The algorithm in this version of GSEA is unchanged from the former code line and produces results equivalent to the previous version (v3.0).</li>
+
* Updates for the '''MSigDB v7.0''' release.
−
    <li dir="ltr" style="list-style-type:disc>GSEA Desktop v4.0.0 requires either Java 11 or Java 8.  Java 11 is preferred; we provide bundles with an embedded OpenJDK 11 JVM for Mac, Windows (64-bit), and Linux.</li>
+
* Updates for compatibility with Java 11 and the (free) OpenJDK version of Java.
−
  </ul>
+
* New options for downloading and launching the application:  
−
</p>
+
** Windows installer, Mac app, and Linux bundle, each with an '''embedded OpenJDK Java 11''', which means no separate Java installation is needed.   
−
<p>
+
** 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.
−
<h3>Improvements</h3>
+
** Note: Launching the application using Java Web Start still requires a '''separate Java 8''' installation.
−
  <ul style="margin-top:0pt;margin-bottom:0pt;">
+
* Miscellaneous performance improvements and code simplifications. These add up to a roughly 40% improvement over v3.0 in our informal testing.
−
    <li dir="ltr" style="list-style-type:disc>Updated for the MSigDB v7.0 release.</li>
+
* 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.
−
    <li dir="ltr" style="list-style-type:disc>Migrated code for Java 11 compatibility and corresponding better security.</li>
+
* Fixed an indefinite wait cursor in the Leading Edge Tool.
−
    <li dir="ltr" style="list-style-type:disc>Performance improvements: we are seeing a roughly 40% improvement in our informal testing.</li>
+
* 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 [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])
−
    <li dir="ltr" style="list-style-type:disc>Created dedicated Windows installer, Mac.app, and Linux bundle, each with an embedded OpenJDK 11 to avoid issues with the user needing to install Java.  Created new command-line scripts for launching the GUI and running batch analyses so the user can avoid needing to deal directly with the more complex Java 11 command-line.</li>
 
−
    <li dir="ltr" style="list-style-type:disc>Removed implicit dependence on out-of-date internal annotation CHIP file. Removed other special CHIP handling code to avoid conflicting with the results of the new symbol conversion from MSigDB 7.0 and better support RNA-Seq workflows. Annotations now come from the CHIP used to collapse, or else from the dataset itself (and are left untouched).</li>
 
−
    <li dir="ltr" style="list-style-type:disc>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.</li>
 
−
    <li dir="ltr" style="list-style-type:disc>Switched from Ant to Gradle for builds.</li>
 
−
    <li dir="ltr" style="list-style-type:disc>Many code simplifications and removal of unnecessary code.</li>
 
−
    <li dir="ltr" style="list-style-type:disc>Fixed an indefinite wait cursor in the Leading Edge Tool.</li>
 
−
  </ul>
 
−
</p>
 

Latest revision as of 05:40, 22 November 2019

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GSEA Desktop v4.0.3 (Nov 2019)

Miscellaneous bug fixes:

  • Fixed CHIP parsing bugs related to empty values, whitespace, null, etc.
  • Fixed a command-line option bug so the "-collapse" parameter is not required.
  • Changed GSEA cache browsers to sort by date.
  • Changed tab order for GMT chooser

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" operation, to map datasets with older symbols to MSigDB's canonical namespace (Ensembl 97 in MSigDB 7.0). 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.
    • Note that the UI around the Collapse function has changed to accommodate this new operation. The former true/false "Collapse dataset to gene symbols" parameter has been changed to "Collapse/Remap to gene symbols", with options "Collapse / No_Collapse / Remap_Only".
    • The various collapse modes are ignored when remapping, and GSEA will report an error if the dataset contains multiple input symbols that map to the same gene in the specified CHIP file. Remap_Only is intended as a symbol conversion step and nothing more.
    • The command-line parameters dealing with the Collapse function remain the same as before but now take these new option values; use the GUI "Command" function to view examples of usage. As a convenience, GSEA will continue to accept "true" and "false" as aliases for "Collapse" and "No_Collapse", respectively.
  • Restoration of the Collapse function to GSEA Preranked.
    • This was removed in the past because the GSEA team could not vouch for the use of any particular collapse mode when dealing with unknown custom user-defined ranking metrics. We have restored it with a default of Remap_Only primarily to support the need to update old datasets to Ensembl 97.
    • Use the other collapse modes with custom ranking metrics at your own discretion. We recommend you consult with a local statistician to make sure any such collapsing steps are valid for your chosen metric, or handling such steps upstream before applying any metric.
  • Command-line fix for passing individual GMTs vs a GenePattern file-list. Use the -gmx option to pass a single file and the new -gmx_file option to pass a GP style list of multiple files.

Again, use the GUI "Command" function to view examples of usage.

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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