Multi-omic Integration and Analysis of cBioPortal and TCGA data with MultiAssayExperiment
Author(s): Marcel Ramos,Levi Waldron,Ludwig Geistlinger
Affiliation(s): CUNY School of Public Health, Roswell Park Comprehensive Cancer Center
This workshop demonstrates how to leverage public multi-omics databases, such as the cBioPortal and The Cancer Genome Atlas (TCGA). Workshop participants are given an overview of the `cBioPortalData`, `curatedTCGAData`, `terraTCGAdata`, and `SingleCellMultiModal`, data packages. It introduces users to minimal data management with `MultiAssayExperiment` and `TCGAutils`, packages that organize and manage multi-omics datasets. The workshop will provide participants with ways to improve the ease-of-use of TCGA data, and introduce them to common Bioconductor data classes including `SummarizedExperiment`, `MultiAssayExperiment`, and `RaggedExperiment`. The workshop will also demonstrate the experimental `terraTCGAdata` package for working with TCGA data on the AnVIL Terra platform, as well as, a review of updates to existing functionality in `cBioPortalData`, `MultiAssayExperiment`, `TCGAutils`, `TENxIO`, and `SingleCellMultiModal`.