Part 1: Multi-omic Integration Of Cbioportal And TCGA Data With Multiassayexperiment
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See Part 2: • Part 2: Multi-omic Integration Of Cbioport...
Marcel Ramos, Research Associate at the ISPH, Adjunct Lecturer at the CUNY SPH, and member of the Bioconductor core development team, gave a workshop at the BioConductor Conference 2022. Ramos’ workshop was on Multi-omic Integration Of Cbioportal And TCGA Data With Multiassayexperiment.
From the Bioconductor Conference 2022
Author(s): Marcel Ramos, Levi Waldron, Ludwig Geistlinger
Affiliation(s): CUNY Graduate School of Public Health and Health Policy
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
https://waldronlab.io/MultiAssayWorks...
Source code
https://github.com/waldronlab/MultiAs...
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