F1000research depmap workflow paper.

Abstract

The depmap package facilitates access in the R environment to the data from the Depmap project, a multi-year collaborative effort by the Broad Institute and Wellcome Sanger Institute, mapping genetic and chemical dependencies and other molecular biological measurements of over 1700 cancer cell lines. The depmap package formats this data for use of popular R data analysis and visualizing tools such as dplyr and ggplot2 to represent and visualize these rich datasets. In addition, the depmap package utilizes ExperimentHub, storing versions of the Depmap data accessible from the Cloud, which may be selectively downloaded, providing a reproducible research framework to support exploiting this data. This paper describes a workflow demonstrating how to access and visualize the Depmap data in R using this package.