Harmonizing and integrating the NCI Genomic Data Commons through accessible, interactive, and cloud-enabled workflows.

ABSTRACT: Cancer data is widely available in repositories such as the National Cancer Institute (NCI) Genomic Data Commons (GDC). These datasets could serve as controls or comparisons in compendium analyses with user data, avoiding the expense and time of generating additional datasets. However, the user must be able to process their new data in the same manner for these comparisons to be useful. This can be non-trivial. Although the executables themselves are usually available in repositories, the GDC pipelines that describe that entire analysis workflow are currently published as text-based standard operating procedures (SOPs). It is difficult to document a computational workflow to the level of detail and accuracy required to reproduce the results. Discrepancies between versions and exclusions of

SUBMITTER: Hung LH 

PROVIDER: S-EPMC11878898 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature