Browse code

fixed link

guangchuang yu authored on 26/09/2016 09:20:07
Showing21 changed files

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@@ -48,7 +48,10 @@ mdfiles:
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 	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
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 	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
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 	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
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-	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")'
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+	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
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+	cd docs;\
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+	ln -f -s ../mysoftware/* ./
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+
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 svnignore:
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 	svn propset svn:ignore -F .svnignore .
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new file mode 100644
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+<!DOCTYPE html>
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+<html lang="en">
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+    <head>
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+        <meta charset="utf-8">
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+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
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+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+        
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+        <meta name="author" content="Guangchuang Yu">
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+        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/ChIPseeker/">
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+        <link rel="shortcut icon" href="../img/favicon.ico">
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+
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+	<title>ChIPseeker - ggtree</title>
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+
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+        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">
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+        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">
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+        <link rel="stylesheet" href="../css/highlight.css">
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+        <link href="../css/base.css" rel="stylesheet">
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+
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+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
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+        <!--[if lt IE 9]>
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+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
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+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
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+        <![endif]-->
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+
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+        
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+        <script>
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+            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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+            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
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+            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
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+
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+            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
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+            ga('send', 'pageview');
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+        </script>
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+        
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+    </head>
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+
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+    <body>
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+
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+    <div class="container">
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+
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+        <!-- Collapsed navigation -->
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+        <div class="navbar-header">
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+            <!-- Expander button -->
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+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
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+                <span class="sr-only">Toggle navigation</span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+            </button>
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+
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+            <!-- Main title -->
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+            <a class="navbar-brand" href="..">ggtree</a>
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+        </div>
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+
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+        <!-- Expanded navigation -->
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+        <div class="navbar-collapse collapse">
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+            <!-- Main navigation -->
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+            <ul class="nav navbar-nav">
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+            
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+            
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+                <li >
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+                    <a href="..">Home</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../documentation/">Documentation</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../faq/">FAQ</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../featuredArticles/">Featured Articles</a>
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+                </li>
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+            
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+            
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+            
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+                <li class="dropdown active">
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+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>
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+                    <ul class="dropdown-menu">
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+                    
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+                        
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+<li class="active">
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+    <a href="./">ChIPseeker</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../clusterProfiler/">clusterProfiler</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../DOSE/">DOSE</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../ggtree/">ggtree</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../GOSemSim/">GOSemSim</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../ReactomePA/">ReactomePA</a>
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+</li>
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+
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+                    
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+                    </ul>
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+                </li>
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+            
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+            
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+            </ul>
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+
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+            <!-- Search, Navigation and Repo links -->
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+            <ul class="nav navbar-nav navbar-right">
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+                <li>
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+                    <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">
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+                        <i class="fa fa-search"></i> Search
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+                    </a>
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+                </li>
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+                <li >
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+                    <a rel="next" href="../featuredArticles/">
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+                        <i class="fa fa-arrow-left"></i> Previous
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+                    </a>
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+                </li>
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+                <li >
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+                    <a rel="prev" href="../clusterProfiler/">
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+                        Next <i class="fa fa-arrow-right"></i>
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+                    </a>
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+                </li>
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+                
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+                <li>
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+                    <a href="https://github.com/GuangchuangYu/ggtree">
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+                        
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+                            <i class="fa fa-github"></i>
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+                        
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+                        GitHub
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+                    </a>
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+                </li>
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+                
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+            </ul>
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+        </div>
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+    </div>
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+</div>
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+
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+        <div class="container">
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+            <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">
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+    <ul class="nav bs-sidenav">
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+    
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+    </ul>
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+</div></div>
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+            <div class="col-md-9" role="main">
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+
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+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ChIPseeker" /></p></div>
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+        </div>
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+
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+        <footer class="col-md-12">
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+            <hr>
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+            
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+                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>
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+            
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+            <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
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+        </footer>
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+
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+        <script src="../js/jquery-1.10.2.min.js"></script>
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+        <script src="../js/bootstrap-3.0.3.min.js"></script>
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+        <script src="../js/highlight.pack.js"></script>
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+        <script>var base_url = '..';</script>
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+        <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script>
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+        <script src="../js/base.js"></script>
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+
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+        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
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+            <div class="modal-dialog">
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+                <div class="modal-content">
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+                    <div class="modal-header">
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+                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
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+                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>
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+                    </div>
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+                    <div class="modal-body">
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+                        <p>
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+                            From here you can search these documents. Enter
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+                            your search terms below.
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+                        </p>
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+                        <form role="form">
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+                            <div class="form-group">
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+                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
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+                            </div>
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+                        </form>
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+                        <div id="mkdocs-search-results"></div>
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+                    </div>
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+                    <div class="modal-footer">
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+                    </div>
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+                </div>
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+            </div>
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+        </div>
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+    </body>
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+</html>
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\ No newline at end of file
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new file mode 100644
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@@ -0,0 +1,216 @@
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+<!DOCTYPE html>
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+<html lang="en">
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+    <head>
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+        <meta charset="utf-8">
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+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
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+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+        
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+        <meta name="author" content="Guangchuang Yu">
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+        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/DOSE/">
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+        <link rel="shortcut icon" href="../img/favicon.ico">
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+
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+	<title>DOSE - ggtree</title>
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+
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+        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">
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+        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">
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+        <link rel="stylesheet" href="../css/highlight.css">
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+        <link href="../css/base.css" rel="stylesheet">
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+
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+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
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+        <!--[if lt IE 9]>
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+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
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+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
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+        <![endif]-->
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+
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+        
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+        <script>
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+            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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+            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
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+            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
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+
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+            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
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+            ga('send', 'pageview');
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+        </script>
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+        
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+    </head>
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+
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+    <body>
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+
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+    <div class="container">
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+
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+        <!-- Collapsed navigation -->
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+        <div class="navbar-header">
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+            <!-- Expander button -->
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+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
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+                <span class="sr-only">Toggle navigation</span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+            </button>
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+
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+            <!-- Main title -->
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+            <a class="navbar-brand" href="..">ggtree</a>
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+        </div>
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+
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+        <!-- Expanded navigation -->
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+        <div class="navbar-collapse collapse">
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+            <!-- Main navigation -->
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+            <ul class="nav navbar-nav">
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+            
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+            
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+                <li >
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+                    <a href="..">Home</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../documentation/">Documentation</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../faq/">FAQ</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../featuredArticles/">Featured Articles</a>
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+                </li>
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+            
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+            
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+            
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+                <li class="dropdown active">
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+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>
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+                    <ul class="dropdown-menu">
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+                    
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+                        
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+<li >
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+    <a href="../ChIPseeker/">ChIPseeker</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../clusterProfiler/">clusterProfiler</a>
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+</li>
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+
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+                    
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+                        
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+<li class="active">
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+    <a href="./">DOSE</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../ggtree/">ggtree</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../GOSemSim/">GOSemSim</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../ReactomePA/">ReactomePA</a>
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+</li>
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+
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+                    
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+                    </ul>
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+                </li>
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+            
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+            
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+            </ul>
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+
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+            <!-- Search, Navigation and Repo links -->
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+            <ul class="nav navbar-nav navbar-right">
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+                <li>
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+                    <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">
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+                        <i class="fa fa-search"></i> Search
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+                    </a>
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+                </li>
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+                <li >
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+                    <a rel="next" href="../clusterProfiler/">
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+                        <i class="fa fa-arrow-left"></i> Previous
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+                    </a>
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+                </li>
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+                <li >
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+                    <a rel="prev" href="../ggtree/">
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+                        Next <i class="fa fa-arrow-right"></i>
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+                    </a>
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+                </li>
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+                
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+                <li>
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+                    <a href="https://github.com/GuangchuangYu/ggtree">
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+                        
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+                            <i class="fa fa-github"></i>
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+                        
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+                        GitHub
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+                    </a>
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+                </li>
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+                
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+            </ul>
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+        </div>
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+    </div>
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+</div>
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+
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+        <div class="container">
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+            <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">
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+    <ul class="nav bs-sidenav">
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+    
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+    </ul>
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+</div></div>
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+            <div class="col-md-9" role="main">
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+
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+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/DOSE" /></p></div>
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+        </div>
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+
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+        <footer class="col-md-12">
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+            <hr>
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+            
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+                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>
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+            
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+            <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
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+        </footer>
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+
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+        <script src="../js/jquery-1.10.2.min.js"></script>
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+        <script src="../js/bootstrap-3.0.3.min.js"></script>
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+        <script src="../js/highlight.pack.js"></script>
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+        <script>var base_url = '..';</script>
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+        <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script>
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+        <script src="../js/base.js"></script>
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+
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+        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
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+            <div class="modal-dialog">
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+                <div class="modal-content">
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+                    <div class="modal-header">
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+                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
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+                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>
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+                    </div>
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+                    <div class="modal-body">
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+                        <p>
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+                            From here you can search these documents. Enter
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+                            your search terms below.
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+                        </p>
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+                        <form role="form">
204
+                            <div class="form-group">
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+                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
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+                            </div>
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+                        </form>
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+                        <div id="mkdocs-search-results"></div>
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+                    </div>
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+                    <div class="modal-footer">
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+                    </div>
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+                </div>
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+            </div>
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+        </div>
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+    </body>
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+</html>
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\ No newline at end of file
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new file mode 100644
... ...
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+<!DOCTYPE html>
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+<html lang="en">
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+    <head>
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+        <meta charset="utf-8">
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+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
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+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+        
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+        <meta name="author" content="Guangchuang Yu">
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+        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/GOSemSim/">
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+        <link rel="shortcut icon" href="../img/favicon.ico">
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+
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+	<title>GOSemSim - ggtree</title>
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+
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+        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">
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+        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">
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+        <link rel="stylesheet" href="../css/highlight.css">
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+        <link href="../css/base.css" rel="stylesheet">
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+
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+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
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+        <!--[if lt IE 9]>
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+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
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+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
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+        <![endif]-->
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+
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+        
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+        <script>
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+            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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+            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
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+            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
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+
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+            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
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+            ga('send', 'pageview');
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+        </script>
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+        
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+    </head>
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+
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+    <body>
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+
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+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+    <div class="container">
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+
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+        <!-- Collapsed navigation -->
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+        <div class="navbar-header">
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+            <!-- Expander button -->
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+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
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+                <span class="sr-only">Toggle navigation</span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+            </button>
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+
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+            <!-- Main title -->
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+            <a class="navbar-brand" href="..">ggtree</a>
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+        </div>
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+
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+        <!-- Expanded navigation -->
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+        <div class="navbar-collapse collapse">
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+            <!-- Main navigation -->
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+            <ul class="nav navbar-nav">
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+            
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+            
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+                <li >
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+                    <a href="..">Home</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../documentation/">Documentation</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../faq/">FAQ</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../featuredArticles/">Featured Articles</a>
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+                </li>
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+            
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+            
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+            
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+                <li class="dropdown active">
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+
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+<li class="active">
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+    <a href="./">clusterProfiler</a>
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+</li>
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+<li >
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+</li>
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+<li >
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+    <a href="../clusterProfiler/">clusterProfiler</a>
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+            <hr>
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+                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>
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0 217
\ No newline at end of file
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90 90
                     
91 91
                         
92 92
 <li >
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-    <a href="../mysoftware/ChIPseeker/">ChIPseeker</a>
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+    <a href="ChIPseeker/">ChIPseeker</a>
94 94
 </li>
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 <li >
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 </li>
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 <li >
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 </li>
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 <li >
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... ...
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182 182
         }, 
183 183
         {
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             "location": "/featuredArticles/", 
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-            "text": "Let us know if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart16f2218d1abb\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart16f2218d1abb\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape \n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens \n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015 \n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species \n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 
185
+            "text": "Let us know if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart223ede02dc5\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart223ede02dc5\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape \n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens \n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015 \n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species \n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 
186 186
             "title": "Featured Articles"
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             "title": " 2015"
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         }, 
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         {
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             "text": "", 
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             "title": "ChIPseeker"
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         }, 
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         {
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             "title": "clusterProfiler"
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         }, 
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         {
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         {
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             "title": "ggtree"
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         {
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             "title": "GOSemSim"
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         {
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-            "location": "/../mysoftware/ReactomePA/", 
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             "title": "ReactomePA"
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... ...
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     <url>
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-     <loc>https://guangchuangyu.github.io/ggtree/../mysoftware/ChIPseeker/</loc>
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+     <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>
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      <lastmod>2016-09-26</lastmod>
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      <changefreq>daily</changefreq>
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     <url>
45
-     <loc>https://guangchuangyu.github.io/ggtree/../mysoftware/clusterProfiler/</loc>
45
+     <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>
46 46
      <lastmod>2016-09-26</lastmod>
47 47
      <changefreq>daily</changefreq>
48 48
     </url>
49 49
         
50 50
     <url>
51
-     <loc>https://guangchuangyu.github.io/ggtree/../mysoftware/DOSE/</loc>
51
+     <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
52 52
      <lastmod>2016-09-26</lastmod>
53 53
      <changefreq>daily</changefreq>
54 54
     </url>
55 55
         
56 56
     <url>
57
-     <loc>https://guangchuangyu.github.io/ggtree/../mysoftware/ggtree/</loc>
57
+     <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
58 58
      <lastmod>2016-09-26</lastmod>
59 59
      <changefreq>daily</changefreq>
60 60
     </url>
61 61
         
62 62
     <url>
63
-     <loc>https://guangchuangyu.github.io/ggtree/../mysoftware/GOSemSim/</loc>
63
+     <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
64 64
      <lastmod>2016-09-26</lastmod>
65 65
      <changefreq>daily</changefreq>
66 66
     </url>
67 67
         
68 68
     <url>
69
-     <loc>https://guangchuangyu.github.io/ggtree/../mysoftware/ReactomePA/</loc>
69
+     <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
70 70
      <lastmod>2016-09-26</lastmod>
71 71
      <changefreq>daily</changefreq>
72 72
     </url>
73 73
new file mode 120000
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@@ -0,0 +1 @@
1
+../mysoftware/ChIPseeker.md
0 2
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1 3
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@@ -0,0 +1 @@
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+../mysoftware/DOSE.md
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+../mysoftware/GOSemSim.md
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+../mysoftware/ReactomePA.md
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1 3
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+../mysoftware/clusterProfiler.md
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... ...
@@ -36,10 +36,10 @@ Let us know if you have published using `ggtree` and your publication will be fe
36 36
   }  
37 37
   </style>
38 38
 
39
-<div id = 'chart16f2218d1abb' class = 'rChart morris'></div>
39
+<div id = 'chart223ede02dc5' class = 'rChart morris'></div>
40 40
 <script type='text/javascript'>
41 41
     var chartParams = {
42
- "element": "chart16f2218d1abb",
42
+ "element": "chart223ede02dc5",
43 43
 "width":            800,
44 44
 "height":            400,
45 45
 "xkey": "year",
... ...
@@ -53,7 +53,7 @@ Let us know if you have published using `ggtree` and your publication will be fe
53 53
 "pubid": "HtEfBTGE9r8C" 
54 54
 } 
55 55
 ],
56
-"id": "chart16f2218d1abb",
56
+"id": "chart223ede02dc5",
57 57
 "labels": "cites" 
58 58
 },
59 59
       chartType = "Bar"
60 60
new file mode 120000
... ...
@@ -0,0 +1 @@
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+../mysoftware/ggtree.md
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\ No newline at end of file
... ...
@@ -11,12 +11,12 @@ pages:
11 11
 - FAQ: faq.md
12 12
 - Featured Articles: featuredArticles.md
13 13
 - My Software:
14
-  - ChIPseeker: ../mysoftware/ChIPseeker.md
15
-  - clusterProfiler: ../mysoftware/clusterProfiler.md
16
-  - DOSE: ../mysoftware/DOSE.md
17
-  - ggtree: ../mysoftware/ggtree.md
18
-  - GOSemSim: ../mysoftware/GOSemSim.md
19
-  - ReactomePA: ../mysoftware/ReactomePA.md
14
+  - ChIPseeker: ChIPseeker.md
15
+  - clusterProfiler: clusterProfiler.md
16
+  - DOSE: DOSE.md
17
+  - ggtree: ggtree.md
18
+  - GOSemSim: GOSemSim.md
19
+  - ReactomePA: ReactomePA.md
20 20
 
21 21
 
22 22
 copyright: Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div>