oncoEnrichR use cases
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<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.v1.4.1.html</em> <em>fgfr1_network_oncoEnrichR.v1.4.1.xlsx</em> EGFRi drug resistance drivers (CRISPR screen) <em>egfr_drug_resistance_oncoEnrichR.v1.4.1.html</em> <em>egfr_drug_resistance_oncoEnrichR.v1.4.1.xlsx</em> <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 <LOCAL_DIRECTORY>/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
**用例分析——oncoEnrichR** 本Zenodo存储库托管了两份来自oncoEnrichR的用例输出报告。oncoEnrichR是一款专门用于癌症基因集注释解读的专用工具。 目录结构如下： 1. **reports** 文件夹：存放两份用例的预计算HTML报告与Excel工作簿： - FGFR1（成纤维细胞生长因子受体1）网络（蛋白质邻近筛选）： *fgfr1_network_oncoEnrichR.v1.4.1.html* *fgfr1_network_oncoEnrichR.v1.4.1.xlsx* - EGFRi（表皮生长因子受体抑制剂）耐药驱动因子（CRISPR筛选）： *egfr_drug_resistance_oncoEnrichR.v1.4.1.html* *egfr_drug_resistance_oncoEnrichR.v1.4.1.xlsx* 2. **input** 文件夹：存放两份用例的输入数据： 1. fgfr1_network_input.tsv 2. egfr_drug_resistance_input.tsv 3. **docker** 文件夹：存放可通过Docker容器重新运行用例分析的输入文件与代码。 操作指南： 1. 在本地计算机（macOS/Linux系统）上安装Docker 2. 将docker目录下的input与output文件夹下载至本地计算机 3. 在命令行执行以下Docker命令拉取镜像： `docker pull sigven/oeusecase:latest` 4. 执行以下Docker命令运行用例分析： `docker run --rm -ti -v <LOCAL_DIRECTORY>/input:/input -v <LOCAL_DIRECTORY>/output:/output sigven/oeusecase:latest` **注意**：请将`LOCAL_DIRECTORY`替换为本地计算机中已下载input与output文件夹的完整路径。 上述命令将在output目录下生成两份用例的HTML报告与Excel工作簿。
