https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main-Update&feed=atom&action=history Main-Update - Revision history 2024-03-28T09:24:32Z Revision history for this page on the wiki MediaWiki 1.34.4 https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main-Update&diff=4241&oldid=prev Acastanza at 22:32, 24 April 2019 2019-04-24T22:32:37Z <p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr class="diff-title" lang="en"> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: #fff; color: #222; text-align: center;">Revision as of 22:32, 24 April 2019</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l18" >Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you have a question, see the [[FAQ]] or the [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide]. The User Guide describes how to prepare data files, load data files, run the gene set enrichment analysis, and interpret the results. It also includes instructions for running GSEA from the command line and a Quick Reference section, which describes each window of the GSEA desktop application. &lt;br /&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If you have a question, see the [[FAQ]] or the [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide]. The User Guide describes how to prepare data files, load data files, run the gene set enrichment analysis, and interpret the results. It also includes instructions for running GSEA from the command line and a Quick Reference section, which describes each window of the GSEA desktop application. &lt;br /&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;/p&gt;</div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;h4&gt;Getting Started with RNA-seq Data&lt;/h4&gt;</ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">&lt;p&gt;&lt;/p&gt;</ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;MSigDB gene sets&lt;/h2&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;h2&gt;MSigDB gene sets&lt;/h2&gt;</div></td></tr> <tr><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt; Current release of the Molecular Signatures Database ([[MSigDB_v6.2_Release_Notes|v6.2 MSigDB]]) contains 17,810 gene sets for use with GSEA. For information about MSigDB and the gene sets, see the [http://www.broadinstitute.org/gsea/msigdb MSigDB web site].  &lt;/p&gt;</div></td><td class='diff-marker'> </td><td style="background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>&lt;p&gt; Current release of the Molecular Signatures Database ([[MSigDB_v6.2_Release_Notes|v6.2 MSigDB]]) contains 17,810 gene sets for use with GSEA. For information about MSigDB and the gene sets, see the [http://www.broadinstitute.org/gsea/msigdb MSigDB web site].  &lt;/p&gt;</div></td></tr> </table> Acastanza https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php?title=Main-Update&diff=4240&oldid=prev Acastanza: Created page with '[http://www.broadinstitute.org/gsea/ GSEA Home] | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures…' 2019-04-23T17:43:48Z <p>Created page with &#039;[http://www.broadinstitute.org/gsea/ GSEA Home] | [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures…&#039;</p> <p><b>New page</b></p><div>[http://www.broadinstitute.org/gsea/ GSEA Home] |<br /> [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] | <br /> [http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] | <br /> [http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |<br /> [http://www.broadinstitute.org/gsea/contact.jsp Contact]<br /> &lt;br&gt;<br /> &lt;p&gt; Use the navigation bar on the left to display documentation on GSEA software, MSigDB database or GSEA/MSigDB web site. If you have comments or questions not answered by the [[FAQ]] or the [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide], contact us at [https://groups.google.com/group/gsea-help groups.google.com/group/gsea-help].&lt;/p&gt;<br /> <br /> &lt;ul&gt; When contacting our team with questions about java GSEA programs, please send the following information:<br /> &lt;li&gt; your computer's operation system<br /> &lt;li&gt; version of java which you used to run GSEA<br /> &lt;li&gt; detailed log transcript from the GSEA session in question<br /> &lt;p&gt; to view the log, click [+] at the bottom of main screen of GSEA java desktop application, copy the text to a separate file and attach it to your request &lt;/p&gt;<br /> &lt;/ul&gt;<br /> <br /> &lt;h2&gt;Where to start&lt;/h2&gt;<br /> &lt;p&gt; If you are new to GSEA, see the [http://www.broadinstitute.org/gsea/doc/desktop_tutorial.jsp Tutorial] for a brief overview of the software. <br /> If you have a question, see the [[FAQ]] or the [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide]. The User Guide describes how to prepare data files, load data files, run the gene set enrichment analysis, and interpret the results. It also includes instructions for running GSEA from the command line and a Quick Reference section, which describes each window of the GSEA desktop application. &lt;br /&gt;<br /> &lt;/p&gt;<br /> &lt;h2&gt;MSigDB gene sets&lt;/h2&gt;<br /> &lt;p&gt; Current release of the Molecular Signatures Database ([[MSigDB_v6.2_Release_Notes|v6.2 MSigDB]]) contains 17,810 gene sets for use with GSEA. For information about MSigDB and the gene sets, see the [http://www.broadinstitute.org/gsea/msigdb MSigDB web site]. &lt;/p&gt;<br /> &lt;p&gt; Please note that gene sets can change or become deprecated in subsequent releases of MSigDB. It is thus important to indicate version of MSigDB to fully reference gene sets used in your study. &lt;/p&gt;<br /> <br /> &lt;h2&gt;Software&lt;/h2&gt;<br /> &lt;p&gt;We provide the following software implementations of the GSEA method:<br /> &lt;ul&gt;<br /> &lt;li&gt;Java desktop application -- Easy-to-use graphical interface that can be run from the [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page. The [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide] fully describes this application (referred to as GSEA or GSEA-P).<br /> &lt;/li&gt;<br /> &lt;li&gt;Java jar file -- Command line interface that can be downloaded from the [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page. See [http://www.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Running_GSEA_from_the Command Line Running GSEA from the Command Line] in the &lt;i&gt;User Guide&lt;/i&gt; for details. This might be useful for analyzing several datasets sequentially, analyzing large datasets, or running analyses on a compute cluster.&lt;/li&gt;<br /> &lt;li&gt;R-GSEA -- R implementation of GSEA that can be downloaded from the [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page. This implementation is intended for experienced computational biologists who want to tweak and play with algorithm. The [[R-GSEA_Readme|R-GSEA Readme]] provides brief instructions and support is limited. Please note that this implementation has not been actively maintained since 2005.&lt;/li&gt;<br /> &lt;/ul&gt;<br /> &lt;/p&gt;<br /> &lt;p&gt;Thank you for your interest in GSEA,&lt;br&gt;<br /> The GSEA Team&lt;/p&gt;</div> Acastanza