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