kelly1210 / depmap

Cancer Dependency Map package

The depmap package

depmap is an R data package that disseminates cancer dependency omics datasets from the Broad Institute website depmap. As the DepMap screening efforts continue, the depmap package will updated on a quarterly basis, in line with the Broad Institute depmap cancer dependency mapping initiative.

• Portal: https://depmap.org/portal/
• Selected publications: see https://depmap.org/portal/depmap/

The github page page is for active development, issue tracking and forking/pulling purposes.

Introduction

The depmap package aims to provide a reproducible research framework to cancer dependency data described by Tsherniak, Aviad, et al. "Defining a cancer dependency map." Cell 170.3 (2017): 564-576.. The depmap package should allow a researcher to easily mine dependency data taken from this cancer genomic study, explore and mine the data.

To get an overview of the package, see the depmap vignette.

Installation

To install depmap, the BiocManager Bioconductor Project Package Manager is required. If BiocManager is not already installed, it will need to be done so beforehand with (within R) install.packages("BiocManager"). Once it is installed, depmap can be installed from Biocondctor:

install.packages("BiocManager")
BiocManager::install("depmap")

To install the version from GitHub, use

install.packages("BiocManager")
BiocManager::install("uclouvain-cbio/depmap")

Questions

Feel also free to open a GitHub issue, in particular for bug reports.

Contributing

Contributions to the package are more than welcome. If you want to contribute to this package, you should follow the same conventions as the rest of the functions. Please do get in touch (preferable opening a github issue) to discuss any suggestions.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.