Software Acknowledgements

From GeneSetEnrichmentAnalysisWiki

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             <td><a href="http://www.jidesoft.com jidesoft.com">Jide Software</a></td>
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             <td><a href="http://www.jidesoft.com">Jide Software</a></td>
             <td>Java/Swing components</td>
             <td>Java/Swing components</td>
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             <td><a href="http://www.oracle.com/technetwork/java/index.html http://www.oracle.com/technetwork/java/index.html">The Java 2 Platform</td>
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             <td><a href="http://www.oracle.com/technetwork/java/index.html">The Java 2 Platform</td>
             <td>Language that the GSEA desktop application is written in</td>
             <td>Language that the GSEA desktop application is written in</td>
             <td>[[image:duke.gif]]</td>
             <td>[[image:duke.gif]]</td>
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             <td><a href="http://www.r-project.org/index.html www.r-project.org">The R programming language</a></td>
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             <td><a href="http://www.r-project.org/index.html">The R programming language</a></td>
             <td>Language that the GSEAP-P-R is written in</td>
             <td>Language that the GSEAP-P-R is written in</td>
             <td>[[image:Rlogo.jpg]]</td>
             <td>[[image:Rlogo.jpg]]</td>
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             <td><a href="http://www.jgoodies.com/ www.jgoodies.com">JGoodies</a></td>
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             <td><a href="http://www.jgoodies.com/">JGoodies</a></td>
             <td>Forms layout and java look and feel</td>
             <td>Forms layout and java look and feel</td>
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             <td>[[image: junit.gif]]</td>
             <td>[[image: junit.gif]]</td>
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             <td><a href="http://jakarta.apache.org/log4j/docs/">log4j</a></td>
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            <p><font size="3">log4j </font></p>
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             <td>Logging toolkit for Java</td>
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            <p><font size="3">[[image:log4j.jpg]]</font></p>
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             <td>[[image:log4j.jpg]]</td>
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            <p><font size="3">Logging toolkit for Java</font></p>
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            <p><font size="3">[http://jakarta.apache.org/log4j/docs/ </font><font size="3">jakarta.apache.org/log4j</font><font size="3">]&nbsp;</font></p>
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             <td><a href="http://jakarta.apache.org/oro/">Oro</a></td>
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            <p><font size="3">Oro</font></p>
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             <td>Regular expressions library in Java</td>
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             <td>[[Image:Oro.logo.gif]]</td>
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            <p><font size="3">Regular expressions library in Java</font></p>
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            <p><font size="3">[http://jakarta.apache.org/oro/ </font><font size="3">jakarta.apache.org/oro</font><font size="3">]&nbsp;</font></p>
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Revision as of 19:31, 16 October 2012

<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> | <a href="http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page">Documentation</a> | <a href="http://www.broadinstitute.org/gsea/contact.jsp">Contact</a>

GSEA implementations use many software tools and libraries, several of which are open source or freely available. Our thanks to their developers.

<tbody> </tbody>
<a href="http://www.jidesoft.com">Jide Software</a> Java/Swing components
<a href="http://www.oracle.com/technetwork/java/index.html">The Java 2 Platform Language that the GSEA desktop application is written in image:duke.gif
<a href="http://www.r-project.org/index.html">The R programming language</a> Language that the GSEAP-P-R is written in image:Rlogo.jpg
<a href="http://www.intellij.com/idea/">Intellij IDEA</a> An awesome integrated development environment for Java image:idea.png
<a href="http://www.jgoodies.com/">JGoodies</a> Forms layout and java look and feel
<a href="http://foxtrot.sourceforge.net/docs/introduction.php">foxtrot</a> Java event handling mechanism for GUI's.
<a href="http://www.dom4j.org/">dom4j</a> XML Parser
<a href="http://www.lowagie.com/iText/">itext</a> Java PDF library image:itext.gif
<a href="http://jakarta.apache.org/poi/hssf/index.html">Jakarta POI (especially HSSF)</a> Java excel reporting image: poi-logo.png
<a href="http://www.object-refinery.com/jfreechart/">JFreeChart</a> Graphing library for Java image: jfreechart.png
<a href="http://www.junit.org/index.htm">JUnit</a> Unit testing API image: junit.gif
<a href="http://jakarta.apache.org/log4j/docs/">log4j</a> Logging toolkit for Java image:log4j.jpg
<a href="http://jakarta.apache.org/oro/">Oro</a> Regular expressions library in Java Image:Oro.logo.gif

Trove

High performance collections library from GNU

trove4j.sourceforge.net 

ECS

Element construction set (a HTML tag library from Apache  <st1:place w:st="on"><st1:city w:st="on">Jakarta</st1:city></st1:place>)

jakarta.apache.org

Xenu link sleuth

Website broken link checker

home.snafu.de/tilman/xenulink

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