F1000research depmap
workflow paper.
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.