Which human genes are implicated in tumor development?
geneOncoX is an R package that address this question through the integration of a number of resources with respect to cancer gene annotations, including, but not limited to:
- IntOGen - compendium of mutational cancer driver genes
- Network of Cancer Genes - collection of curated cancer genes
- CancerMine - text-mined predictions of tumor suppressor genes, proto-oncogenes and cancer drivers
- Cancer Gene Census - manually curated resource on cancer genes (soma and germline)
- DNA repair genes - collection of genes involved in DNA repair
- Genomics England PanelApp - collections of cancer gene panels used in clinical diagnostics
- TSO500 targets - cancer genes targeted by Illumina’s TSO500 gene panel
- F1CDx targets - cancer genes targeted by Foundation One’s F1CDx gene panel
The package offers a few pre-processed datasets, along with metadata, that the user can retrieve and use for their own projects or set-ups. The package utilizes the googledrive R package to download the pre-processed and documented datasets to a local cache directory provided by the user.
Code of Conduct
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.