Software for the integration of multi-omics experiments in Bioconductor

ABSTRACT Multi-omics 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 multi-omics 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 all of the multiple ‘omics data for each cancer tissue in The Cancer Genome Atlas (TCGA) 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 multi-omics data and enhances data science applications of multiple omics datasets.