Difference between revisions of "New Page To Test DB Fix"
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| + | <a href="http://www.broad.mit.edu/gsea/">GSEA Home</a> | <a href="../../software/software_index.html">Software</a> | <a href="../../msigdb/msigdb_index.html">MSigDB</a> | Documentation | <a href="../../resources/resources_index.html">Resources</a> <br /> | ||
| + | <br /> | ||
<p><strong><font size="3">Welcome!</font></strong><font size="3"> </font></p> | <p><strong><font size="3">Welcome!</font></strong><font size="3"> </font></p> | ||
<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/cancer/software/gsea/doc/GSEAUserGuideFrame.htm 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 /> | <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/cancer/software/gsea/doc/GSEAUserGuideFrame.htm 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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<p><strong><font size="3">MSigDB gene sets</font></strong></p> | <p><strong><font size="3">MSigDB gene sets</font></strong></p> | ||
| − | <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 MSigDB page.<br /> | + | <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="../../msigdb/msigdb_index.html">MSigDB</a> page.<br /> |
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<ul> | <ul> | ||
<li> | <li> | ||
| − | <p><font size="3">Desktop application -- Easy-to-use graphical interface that can be run from the Software page. The </font><font size="3">[http://www.broad.mit.edu/cancer/software/gsea/doc/GSEAUserGuideFrame.htm User Guide]</font><font size="3"> fully describes this application.</font></p> | + | <p><font size="3">Desktop application -- Easy-to-use graphical interface that can be run from the <a href="../../software/software_index.html">Software</a> page. The </font><font size="3">[http://www.broad.mit.edu/cancer/software/gsea/doc/GSEAUserGuideFrame.htm User Guide]</font><font size="3"> fully describes this application.</font></p> |
</li> | </li> | ||
</ul> | </ul> | ||
<ul> | <ul> | ||
<li> | <li> | ||
| − | <p><font size="3">Java jar file -- Command line interface that can be downloaded from the Software page. The </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> | + | <p><font size="3">Java jar file -- Command line interface that can be downloaded from the <a href="../../software/software_index.html">Software</a> page. The </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> |
</li> | </li> | ||
<li> | <li> | ||
| − | <p><font size="3">R-GSEA -- R implementation of GSEA that can be downloaded from the Software page. This implementation is intended for experienced programmers who want to tweak and play with algorithm. The [[R-GSEA_Readme|R-GSEA Readme]] provides brief instructions and support is limited.</font></p> | + | <p><font size="3">R-GSEA -- R implementation of GSEA that can be downloaded from the <a href="../../software/software_index.html">Software</a> page. This implementation is intended for experienced programmers who want to tweak and play with algorithm. The [[R-GSEA_Readme|R-GSEA Readme]] provides brief instructions and support is limited.</font></p> |
</li> | </li> | ||
<li> | <li> | ||
Revision as of 10:36, 25 July 2007
<a href="http://www.broad.mit.edu/gsea/">GSEA Home</a> | <a href="../../software/software_index.html">Software</a> | <a href="../../msigdb/msigdb_index.html">MSigDB</a> | Documentation | <a href="../../resources/resources_index.html">Resources</a>
Welcome!
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: gsea@broad.mit.edu.
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.
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="../../msigdb/msigdb_index.html">MSigDB</a> page.
Software
GSEA software is distributed in the following ways:
-
Desktop application -- Easy-to-use graphical interface that can be run from the <a href="../../software/software_index.html">Software</a> page. The User Guide fully describes this application.
-
Java jar file -- Command line interface that can be downloaded from the <a href="../../software/software_index.html">Software</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="../../software/software_index.html">Software</a> page. This implementation is intended for experienced programmers 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
