Introduction
depmap is an R/Bioconductor data package that disseminates cancer dependency omics datasets from the Broad Institute depmap project.
- 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.
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..
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.
Questions can also be posted on the Bioconductor forum.
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.