The Genomics of Drugs Sensitivity in Cancer (GDSC) is one of the largest public resources of information for drug sensitivity in cancer cells and molecular markers of drug response.
gdscIC50 is an R package that fits dose response curves for data from the GDSC project. This package uses the non-linear mixed effects model as described in (Vis, D.J. et al. Pharmacogenomics 2016, 17(7):691-700). Once curves are fitted, the generated IC50 values can be used as input to analysis using gdsctools. These two software libraries are used to generate the dose reponse data and statistical analysis presented on the website http://www.cancerrxgene.org.
You can install the package in R using the devtools library. If you haven’t already installed devtools run the following:
Then install the gdscIC50 package. Building the vignette is recommended.
> devtools::install_github("cancerrxgene/gdscIC50", build_vignettes=TRUE)
Once installed, the vignette gives a guide to the curve fitting process.
> library(gdscIC50) > vignette("gdscIC50")