Shiny web application and R processing scripts for the Breast Cancer PDTX Encyclopaedia (BCaPE).

The Breast Cancer PDTX Encyclopaedia (BCaPE) provides tools for visualizing, querying and downloading data from a large collection of highly molecularly annotated breast cancer patient-derived tumour xenografts (PDTX).

The biobank was developed by Carlos Caldas’ laboratory at the Cancer Research UK Cambridge Institute and represents a powerful resource for pre-clinical breast cancer pharmacogenomic studies, including identification of biomarkers of response or resistance.

The BCaPE portal was developed by Matt Eldridge using the R Shiny web application framework with a MySQL database back end accessed using dplyr and dbplyr, and with interactive visualizations using HighCharts and the highcharter R wrapper.

The source code for the BCaPE Shiny web interface and data processing scripts is available on GitHub and the Shiny web interface is available as a Docker container on Docker Hub.


A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds. Bruna et al., Cell 167, 260 – 274 (2016).