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<a href="http://www.broad.mit.edu/gsea/">GSEA Home</a> |  <a href="http://www.broad.mit.edu/gsea/downloads.jsp">Downloads</a> | <a href="http://www.broad.mit.edu/gsea/msigdb/">Molecular Signatures Database</a> | Documentation | <a href="http://www.broad.mit.edu/gsea/contact.jsp">Contact</a>  <br />
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<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 />
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<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.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html User Guide]</font><font size="3">, contact us: </font><font size="4"><font size="3">[mailto:gsea@broad.mit.edu gsea@broad.mit.edu].</font></font><font size="3"><br />
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<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 />
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<p><strong><font size="3">Where to start</font></strong></p>
<p><strong><font size="3">Where to start</font></strong></p>
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<font size="3"> If you are new to GSEA, see the </font><font size="3">[http://www.broad.mit.edu/gsea/doc/desktop_tutorial.jsp Tutorial] </font><font size="3">for a brief overview of the software. <br />
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<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 />
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If you have a question, see the [[FAQ]] or the </font><font size="3">[http://www.broad.mit.edu/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 />
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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 />
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<p><strong><font size="3">MSigDB gene sets</font></strong></p>
<p><strong><font size="3">MSigDB gene sets</font></strong></p>
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<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.broad.mit.edu/gsea/msigdb">MSigDB</a> page.<br />
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<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 />
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     <p><font size="3">Desktop application -- Easy-to-use graphical interface that can be run from the <a href="http://www.broad.mit.edu/gsea/downloads.jsp">Downloads</a> page. The </font><font size="3">[http://www.broad.mit.edu/gsea/doc/GSEAUserGuideFrame.html User Guide]</font><font size="3"> fully describes this application (referred to as GSEA or GSEA-P).<br />
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     <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 />
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     <p><font size="3">Java jar file -- Command line interface that can be downloaded from the <a href="http://www.broad.mit.edu/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>
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     <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>
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     <p><font size="3">R-GSEA -- R implementation of GSEA that can be downloaded from the <a href="http://www.broad.mit.edu/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 />
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     <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 />
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Revision as of 14:50, 16 July 2009

<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>


Use the navigation bar on the left to display GSEA documentation. If you have comments or questions not answered by the FAQ or the User Guide, contact us: broadinstitute.org gsea@broadinstitute.org.

Where to start

If you are new to GSEA, see the 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
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.

MSigDB gene sets

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.

Software

 GSEA software is distributed in the following ways:

  • 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  User Guide 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.

  • 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 who want to tweak and play with algorithm. The R-GSEA Readme provides brief instructions and support is limited.

  • 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.


Thanks for your interest in GSEA,
The GSEA Team


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