Protocol to set up the CellMinerCDB pharmacogenomics analysis web application with custom cell line data

CellMiner Cross-Database (CellMinerCDB) is an interactive web application for integrating and analyzing molecular and pharmacological data across human cancer cell lines. Here, we detail the setup process, including installing necessary software, preparing compatible datasets, and customizing configuration files; we use sarcoma data as an example. The protocol involves data loading, software configuration, and deployment to enable univariate and multivariate analyses. For complete details on the use and execution of this protocol, please refer to Luna et al. 1 and Tlemsani et al. 2 • Instructions to install a self-hosted CellMiner Cross-Database (CellMinerCDB) instance • Directions to configure with example sarcoma data; applicable to other cell line data • Steps for pharmacogenomics analysis with uni- & multi-variate methods in CellMinerCDB Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. CellMiner Cross-Database (CellMinerCDB) is an interactive web application for integrating and analyzing molecular and pharmacological data across human cancer cell lines. Here, we detail the setup process, including installing necessary software, preparing compatible datasets, and customizing configuration files; we use sarcoma data as an example. The protocol involves data loading, software configuration, and deployment to enable univariate and multivariate analyses.