Analysis of large-scale pharmacogenomic datasets

Over the last few years, a number of pharmacogenomic studies have been conducted to provide the scientific community with two classes of large pharmacogenomic datasets. Drug sensitivity datasets have been developed in the aim of producing detailed genomic profiles of large panels of cancer cell lines and measuring their sensitivity to various anticancer drugs (e.g., CCLE and CGP) . Drug perturbation datasets characterized the transcriptional changes induced by a large set of drugs (e.g., CMAP).

PharmacoGx is an open source package for exploration and joint analyses of multiple pharmacogenomic datasets of both classes (sensitivity and perturbation). This package enables users to download and interrogate large-scale pharmacogenomic datasets that were extensively curated to ensure maximum overlap and consistency between datasets. It encompasses several parallelized functions facilitating the exploration and analysis of large pharmacogenomic datasets.

For now, PharmacoSets objects for CCLE, CGP and CMAP are available through the links below. We will create and add PharmacoSets objects for the other pharmacogenomic studies gradually in near future. Please contact us if you are interested in using PharmacoGx for any specific pharmacogenomic dataset.

Package URL: https://cran.r-project.org/web/packages/PharmacoGx/index.html

Publications: To be announced

Nature paper:
https://www.pmgenomics.ca/bhklab/software/pharmacogx/CCLE_Nature2013.RData
https://www.pmgenomics.ca/bhklab/software/pharmacogx/CGP_Nature2013.RData