PharmacoGx: an R package for analysis of large pharmacogenomic datasets
PharmacoGx: an R package for analysis of large pharmacogenomic datasets
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DOI：
10.1093/bioinformatics/btv723
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发表时间：
2016-04-15
期刊：
影响因子：
5.8
通讯作者：
Haibe-Kains, Benjamin
中科院分区：
文献类型：
--
作者：
Smirnov, Petr;Safikhani, Zhaleh;Haibe-Kains, Benjamin
药物基因组学为药物反应生物标志物的开发和新治疗方案的设计带来了巨大的希望，这是精准医学的关键挑战。然而，这些数据是分散的，缺乏有效获取和分析的标准，从而阻碍了药物遗传学的全部潜力的实现。为了解决这些问题，我们实施了PharmacoGx，这是一个易于使用的开源软件包，用于多个药物基因组学数据集的综合分析。我们展示了我们的软件包在比较大型药物敏感性数据集，如癌症药物敏感性基因组学和癌细胞系百科全书中的实用性。此外，我们还展示了如何使用我们的软件包轻松执行连接图分析。随着药物相关数据的可用性增加，我们的软件包将为药物基因组学数据的荟萃分析开辟新的研究途径。
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 pharmacogenonnics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharnnacogenomic 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 Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug -related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data.