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<!doctype html>
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<title>PRIDE-R by PRIDE-R</title>
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<h1>PRIDE-R</h1>
<p>R libraries for the European Bioinformatics Institute PRIDE project</p>
<p class="view"><a href="https://github.com/PRIDE-R">View My GitHub Profile</a></p>
</header>
<section>
<h1>
<a id="pride-r" class="anchor" href="#pride-r" aria-hidden="true"><span class="octicon octicon-link"></span></a>PRIDE-R</h1>
<p>A collection of R tools to access the European Bioinformatics Institute <a href="http://www.ebi.ac.uk/pride">PRIDE project</a> resources, including <a href="http://www.ebi.ac.uk/pride/ws/archive">PRIDE Archive</a> and <a href="http://wwwdev.ebi.ac.uk/pride/ws/cluster">PRIDE Cluster</a> web services, together with different data products based on them. </p>
<p>Currently, the following projects are ongoing: </p>
<ul>
<li>
<a href="http://pride-r.github.io/prideR">prideR</a>: an R package to access PRIDE Archive and PRIDE Cluster<br>
</li>
<li>
<a href="http://pride-r.github.io/archive-annual-trends/">PRIDE Archive trends</a>: Exploratory data analysis and visualisation of PRIDE Archive submissions trends over the years.<br>
</li>
<li>
<a href="http://pride-r.github.io/project-tagger/">PRIDE Archive project tagger</a>: The PRIDE Archive uses a system of tags to classify datasets. So far these tags are manually assigned by curators. By trying to build a model that predict tags, we want to find out what are behind those tags in terms of dataset metadata and natuarl language description.<br>
</li>
<li>
<a href="http://pride-r.github.io/prideRcompare">prideRcompare</a>: Compare, distance, and clustering for prideR projects.<br>
</li>
</ul>
<h3>
<a id="about-us" class="anchor" href="#about-us" aria-hidden="true"><span class="octicon octicon-link"></span></a>About us</h3>
<p>Find out about us in our GitHub profiles:<br>
<a href="https://github.com/jadianes">Jose A. Dianes</a><br>
<a href="https://github.com/ruiwanguk">Rui Wang</a> </p>
<h3>
<a id="how-to-cite" class="anchor" href="#how-to-cite" aria-hidden="true"><span class="octicon octicon-link"></span></a>How to cite</h3>
<ul>
<li>Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., ... & Hermjakob, H. (2013). <em>The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013</em>. Nucleic acids research, 41(D1), D1063-D1069. <a href="http://www.nature.com/nbt/journal/v32/n3/full/nbt.2839.html">HERE</a><br>
</li>
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