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<title>Common Covid Tasks • CCT</title>
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<div class="page-header"><h1 id="common-covid-tasks">Common Covid Tasks<a class="anchor" aria-label="anchor" href="#common-covid-tasks"></a>
</h1></div>
<p>CCT combines a number of commonly requested covid related tasks into an easy(ish) to use package.</p>
<ul>
<li>Create a node network hierarchy from the <a href="https://github.com/cov-lineages/pango-designation" class="external-link">pangolin</a> lineages and aliases</li>
<li>Cache that data locally in case of remote data or access problems</li>
<li>Query that network for ancestors and descendants of a lineage</li>
<li>Parse <a href="https://github.com/cov-lineages/constellations/" class="external-link">constellations</a> into a easily used table</li>
<li>Parse the <a href="https://covariants.org/" class="external-link">covariants.org</a> variant table</li>
<li>Expand all the variants in that table into their children</li>
<li>Sort lineages by ancestry instead of alnum</li>
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<h2 id="installation-instructions">Installation Instructions<a class="anchor" aria-label="anchor" href="#installation-instructions"></a>
</h2>
<p><em>Clone Git Repository and Install Locally</em></p>
<p><code>install.packages("cct", repos = NULL, type="source")</code></p>
<p>or</p>
<p><code>remotes::install_local("cct")</code></p>
<p><em>Install from Github</em></p>
<p><code>remotes::install_github("TheZetner/cct")</code></p>
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<li><small>Apache License (>= 2)</small></li>
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<h2 data-toc-skip>Developers</h2>
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<li>Adrian Zetner <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-4947-9756" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
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<p>Developed by Adrian Zetner.</p>
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