GenomicDataCommons: a Bioconductor Interface to the NCI Genomic Data Commons

Abstract

The National Cancer Institute (NCI) Genomic Data Commons (Grossman et al. 2016, https://gdc.cancer.gov/) provides the cancer research community with an open and unified repository for sharing and accessing data across numerous cancer studies and projects via a high-performance data transfer and query infrastructure. The Bioconductor project (Huber et al. 2015) is an open source and open development software project built on the R statistical programming environment (R Core Team 2016). A major goal of the Bioconductor project is to facilitate the use, analysis, and comprehension of genomic data. The GenomicDataCommons Bioconductor package provides basic infrastructure for querying, accessing, and mining genomic datasets available from the GDC. We expect that Bioconductor developer and bioinformatics community will build on the GenomicDataCommons package to add higher-level functionality and expose cancer genomics data to many state-of-the-art bioinformatics methods available in Bioconductor.\n\nAvailabilityhttps://github.com/Bioconductor/GenomicDataCommons (& soon in Bioconductor).