cBioPortalData

cBioPortalData accesses study datasets from the cBio Cancer Genomics Portal and provides them as integrated multiomic representations in R/Bioconductor.

Key Features:

• Data Access: Retrieves data from pre-packaged zip/tar files or from the cBioPortal API interface.
• Data Formats: Provides data in either tabular format or as MultiAssayExperiment objects using Bioconductor data representations.
• MultiAssayExperiment Integration: Coordinates diverse experimental assays with clinicopathological data using the MultiAssayExperiment data structure.
• Efficient Data Representation: Enables responsive loading times and analysis capabilities, including out-of-memory data representation for large data sets.

Scientific Applications:

• Multiomic Cancer Research: Supports integrated analysis of genomic, transcriptomic, epigenomic, and other assay data from public oncology databases.
• Pan-Cancer Analysis: Facilitates cross-study comparisons using data from more than 260 public studies including The Cancer Genome Atlas (TCGA) data sets.
• Statistical and Visualization Methods: Enables application of general statistical and plotting methods to extensive multiomic data.

Methodology:

The package accesses the cBioPortal web application programming interface and integrates data using the MultiAssayExperiment data structure to coordinate diverse experimental assays with clinicopathological data.