Main Page

From GeneSetEnrichmentAnalysisWiki

(Difference between revisions)
Jump to: navigation, search
 
(37 intermediate revisions not shown)
Line 1: Line 1:
-
<a href="http://www.broadinstitute.org/gsea/">GSEA Home</a> | <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broadinstitute.org/gsea/msigdb/">Molecular Signatures Database</a> | Documentation | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>  <br />
+
[http://www.broadinstitute.org/gsea/ GSEA Home] |
-
<div> <br />
+
[http://www.broadinstitute.org/gsea/downloads.jsp Downloads] |  
-
<font size="3"> Use the navigation bar on the left to display GSEA documentation. </font><font size="3">If you have comments or questions not answered by the </font><font size="3">[[FAQ]] or the </font><font size="3">[http://www.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html User Guide]</font><font size="3">, contact us: </font><font size="4"><font size="3">[mailto:gsea@</font></font><font size="3">broadinstitute.org</font><font size="4"><font size="3"> gsea@</font></font><font size="3">broadinstitute.org</font><font size="4"><font size="3">].</font></font><font size="3"><br />
+
[http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] |  
-
</font><font size="3"><br />
+
[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |
-
</font>
+
[http://www.broadinstitute.org/gsea/contact.jsp Contact]
-
<p><strong><font size="3">Where to start</font></strong></p>
+
<br>
-
<font size="3"> If you are new to GSEA, see the </font><font size="3">[http://www.</font><font size="3">broadinstitute.org</font><font size="3">/gsea/doc/desktop_tutorial.jsp Tutorial] </font><font size="3">for a brief overview of the software. <br />
+
<p> 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].</p>
-
<br />
+
 
-
If you have a question, see the [[FAQ]] or the </font><font size="3">[http://www.</font><font size="3">broadinstitute.org</font><font size="3">/gsea/doc/GSEAUserGuideFrame.html User Guide]</font><font size="3">. 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. <br />
+
<ul> When contacting our team with questions about java GSEA programs, please send the following information:
-
<br />
+
<li> your computer's operation system
-
</font>
+
<li> version of java which you used to run GSEA
-
<p><strong><font size="3">MSigDB gene sets</font></strong></p>
+
<li> detailed log transcript from the GSEA session in question
-
<font size="3"> The Molecular Signatures Database (MSigDB) contains more than 3000 gene sets for use with GSEA. The best source of information about the gene sets is the <a href="http://www.broadinstitute.org/gsea/msigdb">MSigDB</a> page.<br />
+
<p> 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 </p>
-
<br />
+
</ul>
-
</font>
+
 
-
<p><strong><font size="3">Software</font></strong></p>
+
<h2>Where to start</h2>
-
<p>&nbsp;<font size="3">GSEA software is distributed in the following ways: </font><br />
+
<p> 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.  
 +
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. <br />
</p>
</p>
 +
<h3>Getting started with RNA-seq and GSEA</h3>
 +
The GSEA method was originally developed for analysis of microarray data. In order to best adapt this method for RNA-sequencing data sets the GSEA team has developed a [[Using_RNA-seq_Datasets_with_GSEA|collection of guidelines and suggestions which describe how to properly handle these data.]]
 +
<h2>MSigDB gene sets</h2>
 +
<p> Current release of the Molecular Signatures Database ([[MSigDB_v7.4_Release_Notes|v7.4 MSigDB]]) contains 32,284 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].  </p>
 +
<p> Please note that gene sets can change or become deprecated in subsequent releases of MSigDB. It is thus important to indicate the version of MSigDB to fully reference gene sets used in your study. </p>
 +
 +
<h2>Software</h2>
 +
<p>We provide the following software implementations of the GSEA method:
<ul>
<ul>
-
     <li>
+
     <li>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 in detail.
-
    <p><font size="3">Desktop application -- Easy-to-use graphical interface that can be run from the <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> page. The </font><font size="3">[http://www.</font><font size="3">broadinstitute.org</font><font size="3">/gsea/doc/GSEAUserGuideFrame.html User Guide]</font><font size="3"> fully describes this application (referred to as GSEA or GSEA-P).<br />
+
-
    </font></p>
+
     </li>
     </li>
 +
    <li>Java jar file -- Command line interface that can be downloaded from the [http://www.broadinstitute.org/gsea/downloads.jsp Downloads] page. See [http://software.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Running_GSEA_from Running GSEA from the Command Line] in the <i>User Guide</i> for details. This might be useful for analyzing several datasets sequentially, analyzing large datasets, or running analyses on a compute cluster.</li>
 +
    <li>R-GSEA -- R implementation of GSEA that can be downloaded from the [http://www.broadinstitute.org/gsea/downloads_archive.jsp Archived Downloads] page. This implementation is intended for experienced computational biologists who may want to explore the underlying algorithm. The [[R-GSEA_Readme|R-GSEA Readme]] provides brief instructions and support is limited. Please note that this implementation is not actively maintained or supported.</li>
</ul>
</ul>
-
<ul>
+
</p>
-
    <li>
+
<p>Thank you for your interest in GSEA,<br>
-
    <p><font size="3">Java jar file -- Command line interface that can be downloaded from the <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> page. The&nbsp;</font><font size="3"> User Guide</font><font size="3"> describes how to run GSEA from the command line. This might be useful for analyzing several datasets sequentially, analyzing large datasets, or running analyses on a compute cluster. </font></p>
+
The GSEA Team</p>
-
    </li>
+
-
    <li>
+
-
    <p><font size="3">R-GSEA -- R implementation of GSEA that can be downloaded from the <a href="http://www.broadinstitute.org/gsea/downloads.jsp">Downloads</a> page. This implementation is intended for experienced computational biologists </font><font size="3">who want to tweak and play with algorithm. The [[R-GSEA_Readme|R-GSEA Readme]] provides brief instructions and support is limited.<br />
+
-
    </font></p>
+
-
    </li>
+
-
    <li>
+
-
    <p><font size="3">Java source code -- Source code and JavaDoc for the Java jar file can be downloaded from this page. Links are in the navigation bar to the left.</font></p>
+
-
    </li>
+
-
</ul>
+
-
<br />
+
-
<font size="3">Thanks for your interest in GSEA,<br />
+
-
The GSEA Team<br />
+
-
</font> <br />
+
-
<br />
+
-
</div>
+

Current revision as of 23:38, 30 August 2021

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

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 User Guide, contact us at groups.google.com/group/gsea-help.

    When contacting our team with questions about java GSEA programs, please send the following information:
  • your computer's operation system
  • version of java which you used to run GSEA
  • detailed log transcript from the GSEA session in question

    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

Contents

Where to start

If you are new to GSEA, see the Tutorial for a brief overview of the software. If you have a question, see the FAQ or the 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.

Getting started with RNA-seq and GSEA

The GSEA method was originally developed for analysis of microarray data. In order to best adapt this method for RNA-sequencing data sets the GSEA team has developed a collection of guidelines and suggestions which describe how to properly handle these data.

MSigDB gene sets

Current release of the Molecular Signatures Database (v7.4 MSigDB) contains 32,284 gene sets for use with GSEA. For information about MSigDB and the gene sets, see the MSigDB web site.

Please note that gene sets can change or become deprecated in subsequent releases of MSigDB. It is thus important to indicate the version of MSigDB to fully reference gene sets used in your study.

Software

We provide the following software implementations of the GSEA method:

  • Java desktop application -- Easy-to-use graphical interface that can be run from the Downloads page. The User Guide fully describes this application in detail.
  • Java jar file -- Command line interface that can be downloaded from the Downloads page. See Running GSEA from the Command Line in the User Guide for details. This might be useful for analyzing several datasets sequentially, analyzing large datasets, or running analyses on a compute cluster.
  • R-GSEA -- R implementation of GSEA that can be downloaded from the Archived Downloads page. This implementation is intended for experienced computational biologists who may want to explore the underlying algorithm. The R-GSEA Readme provides brief instructions and support is limited. Please note that this implementation is not actively maintained or supported.

Thank you for your interest in GSEA,
The GSEA Team

Personal tools