PharmacoGx is an R/Bioconductor package we developed to simplify the analysis of large PharmacoGenomic Datasets. All the datasets included in PharmacoDB are available as R objects for analysis using PharmacoGx, with both the pharmacological and molecular data from each study. PharmacoGx incorporates all the annotations of each study available in PharmacoDB, and provides a suite of statistical modeling functions to jointly analyze molecular features and drug dose-response curves.
PharmacoGx is simple to start using once R is installed and running on your system. If its your first time using PharmacoGx, download and install the package and all its dependencies by opening an R console and running the following commands:
After installing for the first time, to load the package you can run the following command in your R session:
To download a PharmacoSet object with all the pharmacological and molecular data for GDSC1000 and begin analysing the data, you can use the following commands.
To learn more about the PharmacoGx package, you can download the full documentation and vignettes through our Bioconductor page: PharmacoGx