Difference between revisions of "Main Page"

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<h1><a name="_Toc127331825">Heading 1</a></h1>
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[http://www.broadinstitute.org/gsea/ GSEA Home] |
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<p class="MsoNormal" style="">Format for body text: <st1:place w:st="on"><st1:city w:st="on">Normal</st1:city></st1:place></p>
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[http://www.broadinstitute.org/gsea/downloads.jsp Downloads] |
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<p class="MsoNormal" style="">Format for headings (examples of each follow):</p>
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[http://www.broadinstitute.org/gsea/msigdb/ Molecular Signatures Database] |
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">* <span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;"></span></span><!--[endif]-->Heading 1</span></p>
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[http://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page Documentation] |
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">* </span></span><!--[endif]-->Heading 2</p>
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[http://www.broadinstitute.org/gsea/contact.jsp Contact]
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">* </span></span><!--[endif]-->Heading 3</p>
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<br>
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<h2><a name="_Toc127331826"></a><a name="_Installing_GenePattern"></a><span style="">Heading 2</span></h2>
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<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>
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<p class="MsoNormal"><st1:place w:st="on"><st1:city w:st="on">Normal</st1:city></st1:place> for body text. Body text When you install GenePattern, you typically install all three components: the server, Java Client, and Web Client. GenePattern can be run standalone, or separated into its client and server components to take advantage of a more powerful compute server. A single installer works for either local or distributed configurations.</p>
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<h3><a name="_Toc127331827"></a><a name="_Starting_the_GenePattern_Java Clien"></a><a name="_Exiting_from_GenePattern"></a><span style="">Heading 3</span></h3>
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<ul> When contacting our team with questions about java GSEA programs, please send the following information:
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<p class="MsoNormal"><st1:place w:st="on"><st1:city w:st="on">Normal</st1:city></st1:place> for body text. </p>
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<li> your computer's operation system
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<h4>Heading 4</h4>
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<li> version of java which you used to run GSEA
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<p class="MsoNormal">Rarely used, but should be supported.</p>
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<li> detailed log transcript from the GSEA session in question
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<h1><a name="_Toc127331828">Bulleted and Numbered Lists</a></h1>
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<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>
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<p class="MsoNormal">For bulleted lists, use</p>
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</ul>
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">* </span></span><!--[endif]-->List Bullet</p>
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<p class="MsoListContinue"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">* </span></span><!--[endif]-->List Bullet&lt;br&gt;&lt;br&gt;List Continue</p>
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<h2>Where to start</h2>
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<p class="MsoListBullet2"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">** </span></span><!--[endif]-->List Bullet 2</p>
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<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.
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<p class="MsoListContinue2"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">** </span></span><!--[endif]-->List Bullet 2&lt;br&gt;&lt;br&gt;List Continue 2</p>
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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 />
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">* </span></span><!--[endif]-->List Bullet</p>
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</p>
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<p class="MsoNormal">For numbered lists, use:</p>
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<h3>Getting started with RNA-seq and GSEA</h3>
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<p class="MsoListNumber"><!--[if !supportLists]--><span style="">1.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number.</p>
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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.]]
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<p class="MsoListNumber"><!--[if !supportLists]--><span style="">2.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number.</p>
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<h2>MSigDB gene sets</h2>
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<p class="MsoListContinue">List Continue</p>
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<p> Current release of the Molecular Signatures Database is divided into two parts, the MSigDB Human Collections, and the MSigDB Mouse collections. Release notes for the current version of the Human collections are available here: ([[MSigDB_v2023.1.Hs_Release_Notes|MSigDB v2023.1.Hs]]) and the release notes for the current version of the Mouse collections are available here: ([[MSigDB_v2023.1.Mm_Release_Notes|MSigDB v2023.1.Mm]]). For information about MSigDB and the gene sets, see the [http://www.broadinstitute.org/gsea/msigdb MSigDB web site]. </p>
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<p class="MsoListNumber2"><!--[if !supportLists]--><span style="">1.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number 2</p>
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<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>
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<p class="MsoListNumber2"><!--[if !supportLists]--><span style="">2.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number 2</p>
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<p class="MsoListContinue2">List Continue 2</p>
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<h2>Software</h2>
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<p class="MsoListNumber"><!--[if !supportLists]--><span style="">3.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number.</p>
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<p>We provide the following software implementations of the GSEA method:
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<p class="MsoListNumber2" style=""><!--[if !supportLists]--><span style="">1.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number 2.</p>
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<ul>
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<p class="MsoListNumber2" style=""><!--[if !supportLists]--><span style="">2.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number 2.</p>
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    <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 class="MsoListNumber"><!--[if !supportLists]--><span style="">4.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number.</p>
+
    </li>
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<p class="MsoNormal">Numbered and bulleted lists can be mixed:</p>
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    <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>
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<p class="MsoListNumber" style=""><!--[if !supportLists]--><span style="">1.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number:</p>
+
    <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>
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<p class="MsoListBullet2"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->List Bullet 2</p>
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</ul>
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<p class="MsoListContinue2">List Continue 2</p>
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</p>
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<p class="MsoListBullet2"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->List Bullet 2</p>
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<p>Thank you for your interest in GSEA,<br>
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<p class="MsoListContinue2">List Continue 2</p>
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The GSEA Team</p>
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<p class="MsoListNumber" style=""><!--[if !supportLists]--><span style="">2.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number.</p>
 
−
<p class="MsoListNumber2" style=""><!--[if !supportLists]--><span style="">1.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number 2</p>
 
−
<p class="MsoListNumber2"><!--[if !supportLists]--><span style="">2.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number 2</p>
 
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<p class="MsoListContinue2">List Continue 2</p>
 
−
<p class="MsoListNumber" style=""><!--[if !supportLists]--><span style="">3.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->List number.</p>
 
−
<h1><a name="_Toc127331829"></a><a name="_Getting_Help"></a><span style="">Text Formats</span></h1>
 
−
<p class="MsoNormal">Within paragraph text, we use a number of character formats:</p>
 
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<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->Hyperlinks: <span class="MsoHyperlink">hyperlink</span></p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span class="brcode"><span style="font-size: 10pt; font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><!--[endif]-->Code and file names: <span class="brcode"><span style="font-size: 10pt;">br_code<o:p></o:p></span></span></p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span class="brGUI"><span style="font-family: Symbol; font-style: normal;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><!--[endif]-->For GUI items, like menus and buttons: <span class="brGUI">br_GUI</span><span class="brGUI"><span style="font-style: normal;"><o:p></o:p></span></span></p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->For menus, we use angle brackets, which need to be preserved: <span class="brGUI">File&gt;Open</span>. </p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span class="brvariable"><span style="font-family: Symbol; font-style: normal; text-decoration: none;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><!--[endif]-->For variables (this looks the same as GUI, but might in the future): <span class="brvariable">br_variable</span><span class="brvariable"><span style="font-style: normal;"><o:p></o:p></span></span></p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->For various reasons, most formats can be bold. So bold needs to be preserved.</p>
 
−
<p class="MsoListContinue">Normal formats: <st1:city w:st="on"><st1:place w:st="on">Normal</st1:place></st1:city>, <span class="brcode"><span style="font-size: 10pt;">br_code, </span></span><span class="brGUI">br_GUI, </span><span class="brvariable">br_variable<o:p></o:p></span></p>
 
−
<p class="MsoListContinue">Bold formats: <st1:city w:st="on"><st1:place w:st="on"><strong style="">Normal</strong></st1:place></st1:city><strong style="">, </strong><span class="brcode"><strong style=""><span style="font-size: 10pt;">br_code, </span></strong></span><span class="brGUI"><strong>br_GUI, </strong></span><span class="brvariable"><strong>br_variable</strong><o:p></o:p></span></p>
 
−
<h1><a name="_Toc127331830"></a><a name="_Working_with_Projects"></a><span style="">Header and Footer</span></h1>
 
−
<p class="MsoNormal">The headers and footers would normally come over to html, but just for completeness, those formats would be</p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]-->Header: <span class="HeaderChar">header text</span></p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span class="FooterChar"><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span></span><!--[endif]-->Footer: <span class="FooterChar">footer text<o:p></o:p></span></p>
 
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<h1><a name="_Toc127331831">Tables and Graphics</a></h1>
 
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<p class="MsoNormal">Tables need to come over cleanly. It&rsquo;s hard to capture all formats, but here&rsquo;s a basic table:</p>
 
−
<table cellspacing="0" cellpadding="0" border="1" class="MsoTableGrid" style="border: medium none ; border-collapse: collapse;">
 
−
    <tbody>
 
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        <tr style="">
 
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            <td width="319" valign="top" style="border: 1pt solid windowtext; padding: 0in 5.4pt; width: 239.4pt;">
 
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            <p class="MsoNormal"><strong style="">Column Header<o:p></o:p></strong></p>
 
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            </td>
 
−
            <td width="319" valign="top" style="border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;">
 
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            <p class="MsoNormal"><strong style="">Column Header<o:p></o:p></strong></p>
 
−
            </td>
 
−
        </tr>
 
−
        <tr style="">
 
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            <td width="319" valign="top" style="border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 239.4pt;">
 
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            <p class="MsoNormal">Blah, blah, blah.</p>
 
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            <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  </span></span></span><!--[endif]-->Bulleted stuff, stuff, stuff.</p>
 
−
            <p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  </span></span></span><!--[endif]-->Stuff, stuff, stuff.</p>
 
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            </td>
 
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            <td width="319" valign="top" style="border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;">
 
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            <p class="MsoNormal">Blah, blah, blah.</p>
 
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            <p class="MsoListNumber" style=""><!--[if !supportLists]--><span style="">1.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  </span></span><!--[endif]-->Numbered stuff, stuff, stuff.</p>
 
−
            <p class="MsoListNumber"><!--[if !supportLists]--><span style="">2.<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><!--[endif]-->Stuff,  stuff, stuff.</p>
 
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            </td>
 
−
        </tr>
 
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        <tr style="">
 
−
            <td width="319" valign="top" style="border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 239.4pt;">
 
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            <p class="MsoNormal">Blah, blah, blah.</p>
 
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            </td>
 
−
            <td width="319" valign="top" style="border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 239.4pt;">
 
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            <p class="MsoNormal">Blah, blah, blah.</p>
 
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            </td>
 
−
        </tr>
 
−
    </tbody>
 
−
</table>
 
−
<p class="MsoNormal"><o:p>&nbsp;</o:p></p>
 
−
<p class="MsoNormal">In Word, graphics are linked in files. They also need to come over:</p>
 
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<p class="MsoNormal"><!--[if gte vml 1]><v:shapetype id="_x0000_t75" coordsize="21600,21600"
 
−
o:spt="75" o:preferrelative="t" path="m@4@5l@4@11@9@11@9@5xe" filled="f"
 
−
stroked="f">
 
−
<v:stroke joinstyle="miter" />
 
−
<v:formulas>
 
−
<v:f eqn="if lineDrawn pixelLineWidth 0" />
 
−
<v:f eqn="sum @0 1 0" />
 
−
<v:f eqn="sum 0 0 @1" />
 
−
<v:f eqn="prod @2 1 2" />
 
−
<v:f eqn="prod @3 21600 pixelWidth" />
 
−
<v:f eqn="prod @3 21600 pixelHeight" />
 
−
<v:f eqn="sum @0 0 1" />
 
−
<v:f eqn="prod @6 1 2" />
 
−
<v:f eqn="prod @7 21600 pixelWidth" />
 
−
<v:f eqn="sum @8 21600 0" />
 
−
<v:f eqn="prod @7 21600 pixelHeight" />
 
−
<v:f eqn="sum @10 21600 0" />
 
−
</v:formulas>
 
−
<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect" />
 
−
<o:lock v:ext="edit" aspectratio="t" />
 
−
</v:shapetype><v:shape id="_x0000_i1025" type="#_x0000_t75" style='width:14.25pt;
 
−
height:14.25pt'>
 
−
<v:imagedata src="file:///C:\DOCUME~1\hkuehn\LOCALS~1\Temp\msohtml1\01\clip_image001.gif"
 
−
o:href="images/icon-file-res.gif" />
 
−
</v:shape><![endif]--><!--[if !vml]--><img width="19" height="19" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" v:shapes="_x0000_i1025" /><!--[endif]--></p>
 
−
<p class="MsoNormal">In rare cases, graphics appear in tables. Here&rsquo;s an example:</p>
 
−
<table cellspacing="0" cellpadding="0" border="1" class="MsoTableGrid" style="border: medium none ; margin-left: 5.4pt; border-collapse: collapse;">
 
−
    <tbody>
 
−
        <tr style="">
 
−
            <td width="72" valign="top" style="border: 1pt solid windowtext; padding: 0in 5.4pt; width: 0.75in;">
 
−
            <p class="MsoNormal"><!--[if gte vml 1]><v:shape id="_x0000_i1026" type="#_x0000_t75"
 
−
            style='width:14.25pt;height:14.25pt'>
 
−
            <v:imagedata src="file:///C:\DOCUME~1\hkuehn\LOCALS~1\Temp\msohtml1\01\clip_image001.gif"
 
−
            o:href="images/icon-file-res.gif" />
 
−
            </v:shape><![endif]--><!--[if !vml]--><img width="19" height="19" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image001.gif" v:shapes="_x0000_i1026" /><!--[endif]--></p>
 
−
            </td>
 
−
            <td width="559" valign="top" style="border-style: solid solid solid none; border-color: windowtext windowtext windowtext -moz-use-text-color; border-width: 1pt 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;">
 
−
            <p class="MsoNormal">Expression dataset (res) </p>
 
−
            </td>
 
−
        </tr>
 
−
        <tr style="">
 
−
            <td width="72" valign="top" style="border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 0.75in;">
 
−
            <p class="MsoNormal"><!--[if gte vml 1]><v:shape id="_x0000_i1027" type="#_x0000_t75"
 
−
            style='width:14.25pt;height:14.25pt'>
 
−
            <v:imagedata src="file:///C:\DOCUME~1\hkuehn\LOCALS~1\Temp\msohtml1\01\clip_image002.gif"
 
−
            o:href="images/icon-file-gct.gif" />
 
−
            </v:shape><![endif]--><!--[if !vml]--><img width="19" height="19" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image002.gif" v:shapes="_x0000_i1027" /><!--[endif]--></p>
 
−
            </td>
 
−
            <td width="559" valign="top" style="border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;">
 
−
            <p class="MsoNormal">Expression dataset (gct)</p>
 
−
            </td>
 
−
        </tr>
 
−
        <tr style="">
 
−
            <td width="72" valign="top" style="border-style: none solid solid; border-color: -moz-use-text-color windowtext windowtext; border-width: medium 1pt 1pt; padding: 0in 5.4pt; width: 0.75in;">
 
−
            <p class="MsoNormal"><!--[if gte vml 1]><v:shape id="_x0000_i1028" type="#_x0000_t75"
 
−
            style='width:13.5pt;height:13.5pt'>
 
−
            <v:imagedata src="file:///C:\DOCUME~1\hkuehn\LOCALS~1\Temp\msohtml1\01\clip_image003.gif"
 
−
            o:href="images/icon-file-pcl.gif" />
 
−
            </v:shape><![endif]--><!--[if !vml]--><img width="18" height="18" alt="" src="file:///C:%5CDOCUME~1%5Chkuehn%5CLOCALS~1%5CTemp%5Cmsohtml1%5C01%5Cclip_image003.gif" v:shapes="_x0000_i1028" /><!--[endif]--></p>
 
−
            </td>
 
−
            <td width="559" valign="top" style="border-style: none solid solid none; border-color: -moz-use-text-color windowtext windowtext -moz-use-text-color; border-width: medium 1pt 1pt medium; padding: 0in 5.4pt; width: 419.4pt;">
 
−
            <p class="MsoNormal">Expression dataset (pcl)</p>
 
−
            </td>
 
−
        </tr>
 
−
    </tbody>
 
−
</table>
 
−
<h1><a name="_Toc127331832">Content</a></h1>
 
−
<p class="MsoNormal">The introduction to each section that has subsections, should provide hyperlinks to the subsections. </p>
 
−
<p class="MsoNormal">This section describes how to work with project directories in GenePattern:</p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]--><a href="#_Opening_a_Project_Directory">Projects Pane</a></p>
 
−
<p class="MsoListBullet"><!--[if !supportLists]--><span style="font-family: Symbol;"><span style="">&middot;<span style="font-family: &quot;Times New Roman&quot;; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span></span><!--[endif]--><a href="#_Opening_a_Project_Directory_1">Opening a Project Directory</a></p>
 
−
<h2><a name="_Toc127331833"></a><a name="_Opening_a_Project_Directory"></a><a name="_Projects_Pane"></a><span style="">Projects Pane</span></h2>
 
−
<p class="MsoNormal">Blah, blah, blah.</p>
 
−
<h2><a name="_Toc127331834"></a><a name="_Opening_a_Project_Directory_1"></a><span style="">Opening a Project Directory</span></h2>
 
−
<p class="MsoNormal">Blah, blah, blah.</p>
 

Latest revision as of 19:18, 3 March 2023

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

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 is divided into two parts, the MSigDB Human Collections, and the MSigDB Mouse collections. Release notes for the current version of the Human collections are available here: (MSigDB v2023.1.Hs) and the release notes for the current version of the Mouse collections are available here: (MSigDB v2023.1.Mm). 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

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