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. Cancer Res; 77(21); e39-42. ©2017 AACR.
References
Jan 14, 2011·Bioinformatics·Riku Louhimo, Sampsa Hautaniemi
Aug 21, 2013·PLoS Computational Biology·Michael LawrenceVincent J Carey
Apr 1, 2014·Bioinformatics·Valerie ObenchainMartin Morgan
Jan 31, 2015·Nature Methods·Wolfgang HuberMartin Morgan
Oct 16, 2015·Briefings in Bioinformatics·Lavanya KannanLevi Waldron
Jan 18, 2017·BMC Bioinformatics·Carles Hernandez-FerrerJuan R González
Jan 21, 2017·Science·Teresa DavoliStephen J Elledge
Citations
Jul 15, 2018·Journal of Molecular Endocrinology·Biswapriya B MisraLaura A Cox
May 28, 2019·Nucleic Acids Research·Fedor KolpakovAlexander Kel
Oct 9, 2019·Journal of Translational Medicine·Mario ZanfardinoMarco Aiello
May 27, 2020·JCO Clinical Cancer Informatics·Vincent J CareyMartin Morgan
Jan 29, 2019·American Journal of Epidemiology·Levi WaldronNicola Segata
May 16, 2019·Metabolomics : Official Journal of the Metabolomic Society·Andreas MockChristel Herold-Mende
Aug 17, 2020·Genes·Claudia KasperEduard Murani
Aug 28, 2020·Medicine·Wei LiuYuan-Hao Wu
Jun 20, 2020·Scientific Reports·Akito IshikawaKazuyoshi Endo
Sep 14, 2018·BMC Bioinformatics·Simon KlauAnne-Laure Boulesteix
Jun 16, 2019·Scientific Data·Mira PavkovicVishal S Vaidya
Apr 23, 2020·Frontiers in Oncology·Guillermo de Anda-Jáuregui, Enrique Hernández-Lemus
Mar 21, 2018·MSystems·Levi Waldron
Jun 18, 2020·Genes·Karol G MakowczenkoTadeusz Kaminski
Oct 30, 2020·JCO Clinical Cancer Informatics·Marcel RamosLevi Waldron
Jan 17, 2021·Scientific Reports·Mario ZanfardinoMonica Franzese
Jun 27, 2019·Cell Reports·Aron GyurisAl Charest
Mar 15, 2021·Bioinformatics·Irzam SarfrazJoshua D Campbell
Mar 23, 2021·Frontiers in Genetics·Nuria PlanellDavid Gomez-Cabrero
Mar 30, 2021·Microbiome·Yue ZhaoW Evan Johnson
Apr 4, 2021·International Journal of Molecular Sciences·Efstathios Iason VlachavasSylvia Nürnberg
Jun 3, 2021·International Journal of Molecular Sciences·Francesco PettiniOttavia Spiga
Jun 25, 2021·International Immunopharmacology·Shizhen Lei, Yi Zhang
Oct 6, 2021·Nature Communications·Anthony MammolitiBenjamin Haibe-Kains