Difference between revisions of "Release Notes"

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<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> |  
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[http://www.broadinstitute.org/gsea/ GSEA Home] |
−
<a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> |  
+
[http://www.broadinstitute.org/gsea/downloads.jsp Downloads] |  
−
<a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> |  
+
[http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] |  
−
<a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page">Documentation</a> |
+
[http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |
−
<a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>
+
[http://www.broadinstitute.org/gsea/contact.jsp Contact]
 
<br>
 
<br>
−
<h3><font color="#3366ff">GSEA Web Site Release Notes</font></h3>
+
 
−
<table height="78" width="639" cellspacing="1" cellpadding="1" border="0" align="" summary="">
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<h3><font color="#3366ff">GSEA Software Release Notes</font></h3>
−
    <tbody>
+
<table width="700" cellspacing="1" cellpadding="1" border="0" align="" height="78" summary="">
 
         <tr>
 
         <tr>
 
             <td><strong>Date</strong></td>
 
             <td><strong>Date</strong></td>
Line 13: Line 13:
 
             <td><strong>Description</strong></td>
 
             <td><strong>Description</strong></td>
 
             <td><strong>Release Notes</strong></td>
 
             <td><strong>Release Notes</strong></td>
−
        </tr>
 
−
        <tr>
 
−
            <td>Apr 2013</td>
 
−
            <td>3.87*</td>
 
−
            <td>Several bug fixes and new functionality.</td>
 
−
            <td>[[Web site v3.87 Release Notes|wiki]]</td>
 
−
        </tr>
 
−
      <tr>
 
−
            <td>Oct 2012</td>
 
−
            <td>3.84</td>
 
−
            <td>Several updates and new functionality.</td>
 
−
            <td></td>
 
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
             <td>Jan 2011</td>
+
             <td>Sep 2022</td>
−
             <td>3.5</td>
+
             <td>4.3.<em>x</em>*<br />
−
             <td>Several bug fixes and some new functionality.</td>
+
             </td>
−
             <td>[[Web site v3.4 Release Notes|wiki]]<br />
+
             <td>Support for the new Mouse MSigDB database and versioning scheme changes.
 
             </td>
 
             </td>
 +
            <td>[[GSEA_v4.3.x_Release_Notes|wiki]]</td>
 
         </tr>
 
         </tr>
−
    </tbody>
 
−
</table>
 
−
 
−
<h3><font color="#3366ff">GSEA Software Release Notes</font></h3>
 
−
<table height="78" width="639" cellspacing="1" cellpadding="1" border="0" align="" summary="">
 
−
    <tbody>
 
 
         <tr>
 
         <tr>
−
             <td><strong>Date</strong></td>
+
             <td>Dec 2021 - Jan 2022</td>
−
             <td><strong>Release</strong></td>
+
             <td>4.2.<em>x</em><br />
−
             <td><strong>Description</strong></td>
+
             </td>
−
             <td><strong>Release Notes</strong></td>
+
            <td>New metric (Spearman) and new collapse mode (Absolute Max), better handling of missing values and many other fixes. Updated to latest Log4J jars to avoid concerns of vulnerabilities in earlier Log4J versions.<br />
 +
            </td>
 +
             <td>[[GSEA_v4.2.x_Release_Notes|wiki]]</td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
             <td>Jan 2013</td>
+
             <td>Jul 2020</td>
−
             <td>2.0.10*</td>
+
             <td>4.1.<em>x</em><br />
−
            <td>Fixed recent FTP access issues </td>
+
             </td>
−
            <td>[[GSEA_v2.0.10._Release_Notes|wiki]]</td>
+
             <td>Improved support for macOS Catalina, updated and improved Enrichment Reports, and numerous bug fixes<br />
−
      </tr>
+
             </td>
−
        <tr>
+
             <td>[[GSEA_v4.1.x_Release_Notes|wiki]]</td>
−
             <td>Dec 2012</td>
 
−
             <td>2.0.9</td>
 
−
            <td>Upgrades and bug fixes </td>
 
−
            <td>[[GSEA_v2.09._Release_Notes|wiki]]</td>
 
−
      </tr>
 
−
      <tr>
 
−
            <td>Oct 2012</td>
 
−
            <td>2.0.8</td>
 
−
            <td>Upgrades and bug fixes </td>
 
−
            <td>[[GSEA_v2.08._Release_Notes|wiki]]</td>
 
−
      </tr>
 
−
        <tr>
 
−
            <td>Sept 2010</td>
 
−
             <td>2.0.7</td>
 
−
            <td>Added support for loading other versions of MSigDB into the browser.</td>
 
−
             <td>[[GSEA  v2.0.7 Release Notes|wiki]]</td>
 
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
             <td>Feb 2010</td>
+
             <td>Aug 2019 - Nov 2019</td>
−
             <td>2.0.6</td>
+
             <td>4.0.<em>x</em><br />
−
             <td>Fixed recent FTP access issues</td>
+
            </td>
−
             <td>[[GSEA  v2.0.6 Release Notes|wiki]]</td>
+
             <td>Updates for MSigDB 7.0, Java 11 compatibility, and better performance<br />
 +
            </td>
 +
             <td>[[GSEA_v4.0.x_Release_Notes|wiki]]</td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
             <td>Dec 2009</td>
+
             <td>Jul 2017</td>
−
             <td>2.0.5</td>
+
             <td>3.0<br />
−
             <td>Update GSEA to run under Java 1.6</td>
+
            </td>
−
             <td>[[GSEA_v2.0.5_Release Notes|wiki]]</td>
+
             <td>Open source release, with numerous improvements and bug fixes<br />
 +
            </td>
 +
             <td>[[GSEA_v3.0_Release_Notes|wiki]]</td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
             <td>Mar 2009</td>
+
             <td>Mar 2015 - Apr 2017</td>
−
             <td>2.0.4</td>
+
             <td>2.2.x<br />
−
            <td>Increased the processing speed of the GSEA algorithm<br />
 
 
             </td>
 
             </td>
−
             <td>[[GSEA_v2.0.4_Release Notes|wiki]]</td>
+
            <td>&nbsp;<br />
 +
            </td>
 +
             <td>[[GSEA_v2.2.x_Release_Notes|wiki]]</td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
             <td>Feb 2009</td>
+
             <td>Jun 2014</td>
−
             <td>2.0.2</td>
+
             <td>2.1.0</td>
−
             <td>Added support for password-protected ftp site</td>
+
             <td>Added Enrichment Map visualization of GSEA results</td>
−
             <td>[[GSEA_v2.0.2_Release Notes|wiki]]</td>
+
             <td>[[GSEA_v2.1.0._Release_Notes|wiki]]</td>
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
−
             <td>Feb 2007</td>
+
             <td>Jan 2007 - Jan 2014</td>
−
             <td>2.0.1</td>
+
             <td>2.0.x<br />
−
             <td>Fixed error running leading edge analysis</td>
+
             </td>
−
             <td>[[GSEA_v2.0.1_Release Notes|wiki]]</td>
+
             <td>&nbsp;<br />
−
        </tr>
+
             </td>
−
        <tr>
+
             <td>[[GSEA_v2.0.x_Release_Notes|wiki]]</td>
−
             <td>Jan 2007</td>
 
−
             <td>2.0</td>
 
−
            <td>Major release with significant enhancements</td>
 
−
            <td>[http://www.broadinstitute.org/gsea/doc/whats_new.jsp html]</td>
 
 
         </tr>
 
         </tr>
 
         <tr>
 
         <tr>
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             <td>1.0</td>
 
             <td>1.0</td>
 
             <td>Initial release</td>
 
             <td>Initial release</td>
−
             <td>Not available</td>
+
             <td>&nbsp;</td>
 
         </tr>
 
         </tr>
−
    </tbody>
 
 
</table>
 
</table>
  
 
<h3><font color="#3366ff">MSigDB Release Notes</font></h3>
 
<h3><font color="#3366ff">MSigDB Release Notes</font></h3>
 
<table height="83" width="637" cellspacing="1" cellpadding="1" border="0" align="" summary="">
 
<table height="83" width="637" cellspacing="1" cellpadding="1" border="0" align="" summary="">
−
    <tbody>
+
        <tr>
−
        <tr>
 
 
             <td><strong>Date</strong></td>
 
             <td><strong>Date</strong></td>
 
             <td><strong>Release</strong></td>
 
             <td><strong>Release</strong></td>
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             <td><strong>Release Notes</strong></td>
 
             <td><strong>Release Notes</strong></td>
 
         </tr>
 
         </tr>
−
         <tr valign="top">
+
      <tr valign="top>
 +
            <td>Mar 2023</td>
 +
            <td>&nbsp;2023.2.Hs*</td>
 +
              <td>Update to Ensembl 110 gene annotation data. Miscellaneous collection updates<br>
 +
              <td><span class="plainlinks">[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Hs/ New Docs Site]</span>
 +
</td>
 +
      </tr>
 +
      <tr valign="top>
 +
            <td>Mar 2023</td>
 +
            <td>&nbsp;2023.2.Mm*</td>
 +
              <td>Update to Ensembl 110 gene annotation data. Miscellaneous collection updates<br>
 +
              <td><span class="plainlinks">[https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_2023.2.Mm/ New Docs Site]</span>
 +
</td>
 +
      </tr>
 +
      <tr valign="top>
 +
            <td>Mar 2023</td>
 +
            <td>&nbsp;2023.1.Hs*</td>
 +
              <td>Update to Ensembl 109 gene annotation data. Miscellaneous collection updates<br>
 +
              <td>[[MSigDB_v2023.1.Hs_Release_Notes|wiki]]</td>
 +
      </tr>
 +
      <tr valign="top>
 +
            <td>Mar 2023</td>
 +
            <td>&nbsp;2023.1.Mm*</td>
 +
              <td>Update to Ensembl 109 gene annotation data. Miscellaneous collection updates<br>
 +
              <td>[[MSigDB_v2023.1.Mm_Release_Notes|wiki]]</td>
 +
      </tr>
 +
      <tr valign="top>
 +
            <td>Sep 2022</td>
 +
            <td>&nbsp;2022.1.Hs</td>
 +
              <td>Human MSigDB under a new versioning scheme<br>
 +
              <td>[[MSigDB_v2022.1.Hs_Release_Notes|wiki]]</td>
 +
      </tr>
 +
      <tr valign="top>
 +
            <td>Sep 2022</td>
 +
            <td>&nbsp;2022.1.Mm</td>
 +
              <td>Initial release of Mouse MSigDB<br>
 +
              <td>[[MSigDB_v2022.1.Mm_Release_Notes|wiki]]</td>
 +
      </tr>
 +
      <tr valign="top>
 +
            <td>Jan 2022</td>
 +
            <td>&nbsp;7.5</td>
 +
              <td><br>
 +
              <td>[[MSigDB_v7.5_Release_Notes|wiki]]</td>
 +
      </tr>
 +
      <tr valign="top>
 +
            <td>Mar 2021</td>
 +
            <td>&nbsp;7.4</td>
 +
              <td><br>
 +
              <td>[[MSigDB_v7.4_Release_Notes|wiki]]</td>
 +
         </tr>
 +
      <tr valign="top>
 +
            <td>Mar 2021</td>
 +
            <td>&nbsp;7.3</td>
 +
              <td>C2:CP:WikiPathways +15; C2:CP:Reactome +15; C3:GTRD +175 (bugfix); C5:GO -88; C5:HPO +319; C7:VAX (new sub-collection); C8: +333<br>
 +
              <td>[[MSigDB_v7.3_Release_Notes|wiki]]</td>
 +
        </tr>
 +
      <tr valign="top>
 +
            <td>Sep 2020</td>
 +
            <td>&nbsp;7.2</td>
 +
              <td>C2:CGP +60; C2:CP:WikiPathways (new sub-collection); C2:CP:Reactome +22; C3:GTRD -176; C5:GO +79, C5:HPO (new sub-collection); C8: +51 (promoted from supplementary)<br>
 +
              <td>[[MSigDB_v7.2_Release_Notes|wiki]]</td>
 +
        </tr>
 +
      <tr valign="top>
 +
            <td>Mar 2020</td>
 +
            <td>&nbsp;7.1</td>
 +
              <td>C2 (+28); C3 (+2904); C5(+196)<br>
 +
              <td>[[MSigDB_v7.1_Release_Notes|wiki]]</td>
 +
        </tr>
 +
      <tr valign="top>
 +
            <td>Aug 2019</td>
 +
            <td>&nbsp;7.0</td>
 +
              <td>C1 (-27); C2 (+738); C5 (+4079); <br>
 +
              <td>[[MSigDB_v7.0_Release_Notes|wiki]]</td>
 +
        </tr>   
 +
      <tr valign="top>
 +
            <td>Jul 2018</td>
 +
            <td>&nbsp;6.2</td>
 +
              <td>C2 (+24)<br>
 +
                    [[Mapping_between_v6.2_and_v6.1_gene_sets|Mapping between v6.2 and v6.1 gene sets]]</td>
 +
              <td>[[MSigDB_v6.2_Release_Notes|wiki]]</td>
 +
        </tr>   
 +
      <tr valign="top>
 +
            <td>Oct 2017</td>
 +
            <td>&nbsp;6.1</td>
 +
              <td>C2 (+7)<br>
 +
                    [[Mapping_between_v6.1_and_v6.0_gene_sets|Mapping between v6.1 and v6.0 gene sets]]</td>
 +
              <td>[[MSigDB_v6.1_Release_Notes|wiki]]</td>
 +
        </tr>   
 +
      <tr valign="top>
 +
            <td>Apr 2017</td>
 +
            <td>&nbsp;6.0</td>
 +
              <td>C2 (+2); C5 (-249)</td>
 +
              <td>[[MSigDB_v6.0_Release_Notes|wiki]]</td>
 +
        </tr>   
 +
      <tr valign="top">
 +
            <td>Oct 2016</td>
 +
            <td>&nbsp;5.2</td>
 +
            <td>C2 (+4); C5 (+4,712)<br>
 +
                    [[Mapping_between_v5.2_and_v5.1_gene_sets|Mapping between v5.2 and v5.1 gene sets]]</td>
 +
            <td>[[MSigDB_v5.2_Release_Notes|wiki]]</td>
 +
        <tr valign="top>
 +
            <td>Jan 2016</td>
 +
            <td>&nbsp;5.1</td>
 +
            <td>C2 (+1); C7 (+2,962)</td>
 +
            <td>  [[MSigDB_v5.1_Release_Notes|wiki]]</td>
 +
        </tr>
 +
        <tr valign="top">
 +
            <td>Mar 2015</td>
 +
            <td>&nbsp;5.0</td>
 +
            <td>H (+50); C2 (+3)<br>
 +
                    [[Mapping_between_v5.0_and_v4.0_gene_sets|Mapping between v5.0 and v4.0 gene sets]]</td>
 +
            <td>[[MSigDB_v5.0_Release_Notes|wiki]]</td>
 +
        </tr>
 +
        <tr valign="top">
 +
            <td>May 2013</td>
 +
            <td>&nbsp;4.0</td>
 +
            <td>C2 (-128); C7 (+1,910)</td>
 +
            <td>[[MSigDB_v4.0_Release_Notes|wiki]]</td>
 +
        </tr>
 +
      <tr valign="top">
 
             <td>Oct 2012</td>
 
             <td>Oct 2012</td>
−
             <td>&nbsp;3.1*</td>
+
             <td>&nbsp;3.1</td>
 
             <td>C2 (+1,578); C4 (-23); C6 (+189)<br>
 
             <td>C2 (+1,578); C4 (-23); C6 (+189)<br>
 
                     [[Mapping_between_v3.1_and_v3.0_gene_sets|Mapping between v3.0 and v3.1 gene sets]]</td>
 
                     [[Mapping_between_v3.1_and_v3.0_gene_sets|Mapping between v3.0 and v3.1 gene sets]]</td>
 
             <td>[[MSigDB_v3.1_Release_Notes|wiki]]</td>
 
             <td>[[MSigDB_v3.1_Release_Notes|wiki]]</td>
 
         </tr>
 
         </tr>
−
         <tr>
+
         <tr valign="top">
 
             <td>Sept 2010</td>
 
             <td>Sept 2010</td>
 
             <td>&nbsp;3.0</td>
 
             <td>&nbsp;3.0</td>
Line 173: Line 260:
 
             <td> [http://www.broadinstitute.org/gsea/doc/msigdb_march_2005_release_notes.pdf pdf]</td>
 
             <td> [http://www.broadinstitute.org/gsea/doc/msigdb_march_2005_release_notes.pdf pdf]</td>
 
         </tr>
 
         </tr>
−
    </tbody>
 
 
</table>
 
</table>
 +
<h3><font color="#3366ff">Web site Release Notes</font></h3>
 +
<table height="78" width="639" cellspacing="1" cellpadding="1" border="0" align="" summary="">
 +
        <tr>
 +
            <td><strong>Date</strong></td>
 +
            <td><strong>Release</strong></td>
 +
            <td><strong>Description</strong></td>
 +
            <td><strong>Release Notes</strong></td>
 +
        </tr>
 +
        <tr>
 +
            <td>Aug 2019</td>
 +
            <td>6.4*</td>
 +
            <td>Upgrades to support v7.0 MSigDB.</td>
 +
            <td>[[Web site v6.4 Release Notes|wiki]]</td>
 +
        </tr>
 +
        <tr>
 +
            <td>Apr 2017</td>
 +
            <td>6.0</td>
 +
            <td>Upgrades to support v6.0 MSigDB.</td>
 +
            <td></td>
 +
        </tr>
 +
          <tr>
 +
            <td>Mar 2015</td>
 +
            <td>5.0</td>
 +
            <td>Upgrades to support v5.0 MSigDB.</td>
 +
            <td></td>
 +
        </tr>
 +
        <tr>
 +
            <td>Jun 2014</td>
 +
            <td>4.05</td>
 +
            <td>Several minor updates</td>
 +
            <td></td>
 +
        </tr>
 +
        <tr>
 +
            <td>Apr 2013</td>
 +
            <td>3.87</td>
 +
            <td>Several bug fixes and new functionality.</td>
 +
            <td>[[Web site v3.87 Release Notes|wiki]]</td>
 +
        </tr>
 +
      <tr>
 +
            <td>Oct 2012</td>
 +
            <td>3.84</td>
 +
            <td>Several updates and new functionality.</td>
 +
            <td></td>
 +
        </tr>
 +
        <tr>
 +
            <td>Jan 2011</td>
 +
            <td>3.5</td>
 +
            <td>Several bug fixes and some new functionality.</td>
 +
            <td>[[Web site v3.4 Release Notes|wiki]]<br />
 +
            </td>
 +
        </tr>
 +
</table>
 +
 
<br />
 
<br />
 
<hr>
 
<hr>
 
* Current release <br />
 
* Current release <br />

Latest revision as of 15:55, 20 October 2023

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

GSEA Software Release Notes

Date Release Description Release Notes
Sep 2022 4.3.x*
 Support for the new Mouse MSigDB database and versioning scheme changes. wiki
Dec 2021 - Jan 2022 4.2.x
 New metric (Spearman) and new collapse mode (Absolute Max), better handling of missing values and many other fixes. Updated to latest Log4J jars to avoid concerns of vulnerabilities in earlier Log4J versions.
 wiki
Jul 2020 4.1.x
 Improved support for macOS Catalina, updated and improved Enrichment Reports, and numerous bug fixes
 wiki
Aug 2019 - Nov 2019 4.0.x
 Updates for MSigDB 7.0, Java 11 compatibility, and better performance
 wiki
Jul 2017 3.0
 Open source release, with numerous improvements and bug fixes
 wiki
Mar 2015 - Apr 2017 2.2.x
  
 wiki
Jun 2014 2.1.0 Added Enrichment Map visualization of GSEA results wiki
Jan 2007 - Jan 2014 2.0.x
  
 wiki
Mar 2005 1.0 Initial release  

MSigDB Release Notes

Date Release Description Release Notes
Mar 2023  2023.2.Hs* Update to Ensembl 110 gene annotation data. Miscellaneous collection updates
New Docs Site
Mar 2023  2023.2.Mm* Update to Ensembl 110 gene annotation data. Miscellaneous collection updates
New Docs Site
Mar 2023  2023.1.Hs* Update to Ensembl 109 gene annotation data. Miscellaneous collection updates
wiki
Mar 2023  2023.1.Mm* Update to Ensembl 109 gene annotation data. Miscellaneous collection updates
wiki
Sep 2022  2022.1.Hs Human MSigDB under a new versioning scheme
wiki
Sep 2022  2022.1.Mm Initial release of Mouse MSigDB
wiki
Jan 2022  7.5
wiki
Mar 2021  7.4
wiki
Mar 2021  7.3 C2:CP:WikiPathways +15; C2:CP:Reactome +15; C3:GTRD +175 (bugfix); C5:GO -88; C5:HPO +319; C7:VAX (new sub-collection); C8: +333
wiki
Sep 2020  7.2 C2:CGP +60; C2:CP:WikiPathways (new sub-collection); C2:CP:Reactome +22; C3:GTRD -176; C5:GO +79, C5:HPO (new sub-collection); C8: +51 (promoted from supplementary)
wiki
Mar 2020  7.1 C2 (+28); C3 (+2904); C5(+196)
wiki
Aug 2019  7.0 C1 (-27); C2 (+738); C5 (+4079);
wiki
Jul 2018  6.2 C2 (+24)
Mapping between v6.2 and v6.1 gene sets		 wiki
Oct 2017  6.1 C2 (+7)
Mapping between v6.1 and v6.0 gene sets		 wiki
Apr 2017  6.0 C2 (+2); C5 (-249) wiki
Oct 2016  5.2 C2 (+4); C5 (+4,712)
Mapping between v5.2 and v5.1 gene sets		 wiki
Jan 2016  5.1 C2 (+1); C7 (+2,962) wiki
Mar 2015  5.0 H (+50); C2 (+3)
Mapping between v5.0 and v4.0 gene sets		 wiki
May 2013  4.0 C2 (-128); C7 (+1,910) wiki
Oct 2012  3.1 C2 (+1,578); C4 (-23); C6 (+189)
Mapping between v3.0 and v3.1 gene sets		 wiki
Sept 2010  3.0 C1 (-60); C2 (+1,380); C3 (-1); C4 (-2)
Mapping between v2.5 and v3.0 gene sets		 wiki
April 2008  2.5 C2 (+205); C4 (+456); C5 (+1454)
wiki
Feb 2007  2.1 Minor updates to MSigDB v2.0 annotations
Jan 2007  2.0 C1 (updated); C2 (+269); C3 (+214)
Mapping between v1 and v2 gene sets		 wiki
Nov 2005  1.1 C1 (updated); C2 (+350); C3 (+566); C4
 pdf
March 2005  1.0 Initial release
pdf

Web site Release Notes

Date Release Description Release Notes
Aug 2019 6.4* Upgrades to support v7.0 MSigDB. wiki
Apr 2017 6.0 Upgrades to support v6.0 MSigDB.
Mar 2015 5.0 Upgrades to support v5.0 MSigDB.
Jun 2014 4.05 Several minor updates
Apr 2013 3.87 Several bug fixes and new functionality. wiki
Oct 2012 3.84 Several updates and new functionality.
Jan 2011 3.5 Several bug fixes and some new functionality. wiki


  • Current release
Retrieved from "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Release_Notes&oldid=4562"