Long workshop: Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment

Multi-omic Integration of cBioPortal and TCGA data with MultiAssayExperiment

Marcel Ramos, Levi Waldron, Ludwig Geistlinger

CUNY Graduate School of Public Health and Health Policy

Abstract

This workshop demonstrates the leveraging of public multi-omics databases, such as cBioPortal and The Cancer Genome Atlas (TCGA), through an overview of the cBioPortalData and curatedTCGAData experiment data packages. It introduces users to minimal data management with MultiAssayExperiment and TCGAutils, packages that organize and manage multi-omics datasets. The workshop aims to improve the ease-of-use of TCGA data, and introduce participants to common Bioconductor data structures including SummarizedExperiment, MultiAssayExperiment and RaggedExperiment. The workshop will also mention soon-to-be-released updates to MultiAssayExperiment such as renaming primary identifiers, column names, splitting assays, and maftools compatibility.

Keywords: Data Representation, Infrastructure, cBioPortal, MultiOmic Integration

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