DepMap

DepMap provides programmatic access to DepMap cancer dependency omics datasets for analysis of genetic and chemical dependencies across over 1700 cancer cell lines.

Key Features:

• Molecular datasets: Contains genetic and chemical dependency omics data mapping dependencies across over 1700 cancer cell lines.
• R integration: Supplies R-formatted datasets for analysis within the R environment and compatibility with dplyr and ggplot2.
• ExperimentHub versioning: Stores versioned DepMap datasets on ExperimentHub to enable selective download of specific dataset versions.
• Update cadence: Package datasets are updated quarterly in alignment with DepMap releases.

Scientific Applications:

• Dependency discovery: Enables exploration of genetic and chemical vulnerabilities in cancer cell lines to identify dependencies.
• Target identification: Supports identification and prioritization of potential therapeutic targets from dependency data.
• Data analysis and visualization: Facilitates analysis and visualization of DepMap datasets within R using tools such as dplyr and ggplot2.
• Precision oncology research: Supports hypothesis generation and testing relevant to personalized medicine and targeted therapy development.

Methodology:

The package is updated quarterly and distributes versioned DepMap datasets via ExperimentHub; the underlying data derive from the Broad Institute and Wellcome Sanger Institute collaborative comprehensive screening of cancer cell lines to identify genetic and chemical dependencies.