Ji Hongchao/MetaMapR

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<h1 class="title">README</h1>
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<div id="metamapr" class="section level1">
<h1><a href="http://dgrapov.github.io/MetaMapR/">MetaMapR</a></h1>
<div id="a-metabolomic-network-mapping-tool" class="section level2">
<h2>A metabolomic network mapping tool</h2>
<p><img src="Manual/metamapr_long.gif" alt="demo" /></p>
</div>
<div id="screenshots" class="section level2">
<h2><a href="https://github.com/dgrapov/MetaMapR/blob/master/screenshots.md">Screenshots</a></h2>
<div id="installation" class="section level3">
<h3>Installation</h3>
<p>Requires <a href="http://cran.us.r-project.org/">R</a> and <a href="https://github.com/rstudio/shiny-server">Shiny</a>. Try it out using the <a href="http://spark.rstudio.com/dgrapov/MetaMapR/">Shiny glimmer server</a> or run locally by pasting the following code into the R console:</p>
<pre class="r"><code>library(shiny)
shiny::runGitHub(&#39;MetaMapR&#39;,&#39;dgrapov&#39;)</code></pre>
<p>Alternatively download the .zip file, unzip and run the following code (example for file on desktop)</p>
<pre class="r"><code>library(shiny)
shiny::runApp(&#39;~/../Desktop/MetaMapR-master/MetaMapR-master&#39;)</code></pre>
<p>NOTE: modify file paths for OSX and LINUX</p>
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<div id="instructions" class="section level3">
<h3>Instructions</h3>
<ul>
<li><a href="http://ufpr.dl.sourceforge.net/project/metamapr/Metmapr%20v1.2.1%20tutorial%20v1.doc.pdf">Tutorial</a> (a more detailed version coming soon)</li>
<li><a href="http://dgrapov.github.io/MetaMapR/">Examples</a></li>
</ul>
</div>
<div id="information" class="section level3">
<h3>Information</h3>
<p>Version: 1.4.0 (1/18/2015)</p>
<p>News: <a href="https://github.com/dgrapov/MetaMapR/blob/master/NEWS.md">See the newest features.</a></p>
<p>License: GNU General Public License (v3), <a href="https://github.com/dgrapov/MetaMapR/blob/master/LICENSE">read more</a></p>
</div>
<div id="citation" class="section level3">
<h3>Citation</h3>
<p>If you find MetaMapR useful please cite this tool using the doi listed below.</p>
<p>Dmitry Grapov (2014) MetaMapR: Metabolomic Network Analysis and Visualization Tool</p>
<p><a href="http://dx.doi.org/10.5281/zenodo.12880"><img src="https://zenodo.org/badge/7400/dgrapov/MetaMapR.png" alt="DOI" /></a></p>
</div>
<div id="todo" class="section level3">
<h3>TODO</h3>
<ul>
<li>add partial correlations</li>
<li>add cytoscape.js networks</li>
<li>enable network mapping</li>
</ul>
</div>
<div id="faq" class="section level3">
<h3>FAQ</h3>
<ol style="list-style-type: decimal">
<li>How are multiple edge types handled in the network output?</li>
</ol>
<p>The default setting for returning all edge types or only unique edges can be found under the network tab using the unique edges checkbox. If the option is selected then edges are returned based on a hierarchy Biochemical &gt; Structural &gt; Mass Spectral &gt; Correlation, otherwise all edges are returned.</p>
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Ji Hongchao / MetaMapR

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Ji Hongchao / MetaMapR