Multi-omic Integration Of Cbioportal And TCGA Data With Multiassayexperiment**

Multi-omic Integration Of Cbioportal And TCGA Data With Multiassayexperiment**


Author(s): Marcel Ramos, Levi Waldron, Ludwig Geistlinger

Affiliation(s): CUNY Graduate School of Public Health and Health Policy

Twitter: @M2RuseR

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`, and `terraTCGAdata` (experimental) 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`, and `TCGAutils`.

Workshop details

Source code

Orchestra

1. Go to Orchestra.
2. Log in.
3. Search for the workshop of interest.
4. Click "Launch" (may take a minute or two).
5. Follow instructions.