oncoEnrichR use cases

<strong>Use case analyses - oncoEnrichR</strong> This Zenodo repository hosts two use case output reports from oncoEnrichR, a dedicated tool for geneset interpretation in cancer. Directory structure: <strong><em>reports </em></strong>- holds pre-computed HTML reports and Excel woorkbooks for two use cases FGFR1 network (protein proximity screen) <em>fgfr1_network_oncoEnrichR.v1.4.0.html</em> <em>fgfr1_network_oncoEnrichR.v1.4.0.xlsx</em> EGFRi drug resistance drivers (CRISPR screen) egfr_drug_resistance_oncoEnrichR.v1.4.0html egfr_drug_resistance_oncoEnrichR.v1.4.0.xlsx <em><strong>input </strong></em>- holds input data for the two use cases<br> 1. fgfr1_network_input.tsv<br> 2. egfr_drug_resistance_input.tsv <em><strong>docker</strong></em> - holds input and code for re-running use case analyses through<br> a Docker container Instructions Install Docker on your local computer/client (OS X/Linux) Download the <em>input</em> and <em>output</em> directory of the <em>docker</em> directory to your local computer/client Pull the Docker image with the following Docker command on the command-line: <em>docker pull sigven/oeusecase:latest</em> Run the use case analyses with the following Docker command: <em>docker run --rm -ti -v &lt;LOCAL_DIRECTORY&gt;/input:/input -v /LOCAL_DIRECTORY/output:/output sigven/oeusecase:latest</em> <strong>NOTE</strong>: replace <em>LOCAL_DIRECTORY</em> with the full path on your local computer where you have downloaded the <em>input</em> and <em>output</em> folders The above command will generate HTML reports and Excel workbooks for the two use cases in the <em>output</em> directory