Software for the integration of multiomics experiments in bioconductor

Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, Phil Chapman, Sean R. Davis, David Gomez-Cabrero, Aedin C. Culhane, Benjamin Haibe-Kains, Kasper D. Hansen, Hanish Kodali, Marie S. Louis, Arvind S. Mer, Markus Riester, Martin Morgan, Vince Carey, Levi Waldron

Research output: Contribution to journalArticlepeer-review

28 Scopus citations

Abstract

Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data. We provide the unrestricted multiple 'omics data for each cancer tissue in The Cancer Genome Atlas as ready-to-analyze MultiAssayExperiment objects and demonstrate in these and other datasets how the software simplifies data representation, statistical analysis, and visualization. The MultiAssayExperiment Bioconductor package reduces major obstacles to efficient, scalable, and reproducible statistical analysis of multiomics data and enhances data science applications of multiple omics datasets.
Original languageEnglish (US)
Pages (from-to)e39-e42
Number of pages1
JournalCancer Research
Volume77
Issue number21
DOIs
StatePublished - Jan 1 2017
Externally publishedYes

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