oncoEnrichR use cases

<p><strong>Use case analyses - oncoEnrichR</strong></p> <p>This Zenodo repository hosts two use case output reports from&nbsp;<a href="https://github.com/sigven/oncoEnrichR">oncoEnrichR</a>, a dedicated tool for geneset interpretation in cancer.</p> <p>Directory structure:</p> <ul> <li><strong><em>reports </em></strong>- holds pre-computed HTML reports and Excel woorkbooks for two use cases <ul> <li>FGFR1 network (protein proximity screen) <ul> <li><em>fgfr1_network_oncoEnrichR.v1.4.1.html</em></li> <li><em>fgfr1_network_oncoEnrichR.v1.4.1.xlsx</em></li> </ul> </li> <li>EGFRi drug resistance drivers (CRISPR screen) <ul> <li><em>egfr_drug_resistance_oncoEnrichR.v1.4.1.html</em></li> <li><em>egfr_drug_resistance_oncoEnrichR.v1.4.1.xlsx</em></li> </ul> </li> </ul> </li> </ul> <p>&nbsp;</p> <ul> <li><em><strong>input&nbsp;</strong></em>- holds input data for the two use cases<br> &nbsp; 1. fgfr1_network_input.tsv<br> &nbsp; 2. egfr_drug_resistance_input.tsv</li> </ul> <p>&nbsp;</p> <ul> <li><em><strong>docker</strong></em>&nbsp;- holds input and code for re-running use case analyses through<br> &nbsp; a Docker container <ul> <li>Instructions <ul> <li><a href="https://docs.docker.com/get-docker/">Install Docker</a>&nbsp;on your local computer/client (OS X/Linux)</li> <li>Download the <em>input</em>&nbsp;and <em>output</em>&nbsp;directory of the <em>docker</em>&nbsp;directory to your local computer/client</li> <li>Pull the Docker image with the following Docker command on the command-line: <ul> <li><em>docker pull sigven/oeusecase:latest</em></li> </ul> </li> <li>Run the use case analyses with the following Docker command: <ul> <li><em>docker run --rm -ti -v &lt;LOCAL_DIRECTORY&gt;/input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest</em></li> <li><strong>NOTE</strong>: replace <em>LOCAL_DIRECTORY</em>&nbsp;with the full path on your local computer where you have downloaded the <em>input</em> and <em>output</em> folders</li> <li>The above command will generate HTML reports and Excel workbooks for the two use cases in the <em>output</em> directory</li> </ul> </li> </ul> </li> </ul> </li> </ul>