Analysis of large-scale pharmacogenomic datasets

Description: Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine.However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address theseissues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysisof multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the CancerCell Line Encyclopedia. Moreover, we show how to use our package to easily perform ConnectivityMap analysis. With increasing availability of drug-related data, our package will open new avenuesof research for meta-analysis of pharmacogenomic data.
Authors: Petr Smirnov, Zhaleh Safikhani, Mark Freeman, Benjamin Haibe-Kains
Lab: Haibe-Kains
Version: 1.16.0
Keywords: PharmacoGx, biomarkers, drug response, pharmacogenomics, datasets, ConnectivityMap, statistical analysis, annotations, visualization, R
Licensing: Artistic-2.0


Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., ... & Beck, A. H. (2016). PharmacoGx: an R package for analysis of large pharmacogenomic datasets. Bioinformatics, 32(8), 1244-1246.