Source code repository for the publication Bruna et al., Cell 167, 260 - 274 (2016) and accompanying BCaPE website.
R scripts for carrying out an analysis of the association between various biomarkers and drug sensitivity within a biobank of breast cancer patient-derived tumour xenografts (PDTX) are contained within the processing folder. Instructions for obtaining the mutation, copy number, expression and methylation data, running the sensitivity analysis and creating the database that is used by the BCaPE web application can be found here.
R code for the Shiny application used to create the BCaPE website is available in the shiny folder. Instructions for deploying the Shiny application can be found here.