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<h1 class="title toc-ignore">Code resources accompanying Urbut <em>et al</em>, 2017</h1>
<h4 class="author"><em>Sarah Urbut, Gao Wang, Peter Carbonetto and Matthew Stephens</em></h4>
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<p><strong>Last updated:</strong> 2018-06-04</p>
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Re-built home page with new navbar.
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2018-05-31
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2018-05-22
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2018-05-14
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Added step to install packages in instructions (index.Rmd).
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Setting up workflowr settings.
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Peter Carbonetto
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Setting up workflowr settings.
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Update figures
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2017-09-20
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Moved doc to docs.
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<p></details></p>
<hr />
<div id="overview" class="section level2">
<h2>Overview</h2>
<p>This repository contains code resources to accompany our research paper:</p>
<blockquote>
<p>Sarah M. Urbut, Gao Wang and Matthew Stephens (2017). <em>Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions.</em> bioRxiv <a href="http://dx.doi.org/10.1101/096552">doi:10.1101/096552</a>.</p>
</blockquote>
<p>We provide three sets of code resources:</p>
<ol style="list-style-type: decimal">
<li><p>If you are primarily interested in applying the multivariate adaptive shrinkage (<em>mash</em>) methods to your own data, please see the <a href="https://github.com/stephenslab/mashr">mashr repository</a>.</p></li>
<li><p>If you are working with association statistics from the <a href="http://gtexportal.org">GTEx study</a>, or similar genetic association data, please see <a href="fastqtl2mash.html">here</a> for our code to convert association statistics in the <a href="http://fastqtl.sourceforge.net">FastQTL</a> format, or a similar format, to a format that is more suitable for analysis with <em>mashr</em>.</p></li>
<li><p>If you would like follow the exact steps we took to produce the results of the GTEx analysis presented in the manuscript, follow the instructions <a href="gtex.html">here</a>.</p></li>
</ol>
</div>
<div id="citing-this-work" class="section level2">
<h2>Citing this work</h2>
<p>If you find any of the source code in this repository useful for your work, please cite our manuscript, Urbut <em>et al</em> (2017). The full citation is given above.</p>
</div>
<div id="license" class="section level2">
<h2>License</h2>
<p>Copyright (c) 2016-2018, Sarah Urbut, Gao Wang, Peter Carbonetto and Matthew Stephens.</p>
<p>All source code and software in this repository are made available under the terms of the <a href="https://opensource.org/licenses/mit-license.html">MIT license</a>.</p>
</div>
<div id="whats-included" class="section level2">
<h2>What’s included</h2>
<p><em>Fill out this section.</em></p>
</div>
<div id="contributors" class="section level2">
<h2>Contributors</h2>
<p>This project was developed by <a href="https://github.com/surbut">Sarah Urbut</a>, <a href="https://github.com/gaow">Gao Wang</a>, <a href="http://pcarbo.github.io">Peter Carbonetto</a> and <a href="https://stephenslab.uchicago.edu">Matthew Stephens</a> at the University of Chicago.</p>
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