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Software for the integration of multi-omics experiments in Bioconductor

Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez Cabrera, Tiffany Chan, Philip Chapman, View ORCID ProfileSean Davis, View ORCID ProfileDavid Gomez-Cabrero, View ORCID ProfileAedin C. Culhane, View ORCID ProfileBenjamin Haibe-Kains, View ORCID ProfileKasper D. Hansen, Hanish Kodali, Marie Stephie Louis, Arvind Singh Mer, View ORCID ProfileMarkus Riester, Martin Morgan, Vincent Carey, View ORCID ProfileLevi Waldron
doi: https://doi.org/10.1101/144774
Marcel Ramos
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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Lucas Schiffer
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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Angela Re
3Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Trento, Italy
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Rimsha Azhar
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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Azfar Basunia
4Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
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Carmen Rodriguez Cabrera
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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Tiffany Chan
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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Philip Chapman
5Computational Biology Support Team, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, UK
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Sean Davis
6Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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  • ORCID record for Sean Davis
David Gomez-Cabrero
7Mucosal and Salivary Biology Division, King's College London Dental Institute, London, UK
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  • ORCID record for David Gomez-Cabrero
Aedin C. Culhane
4Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
8Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA (was 16)
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Benjamin Haibe-Kains
9Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
10Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
11Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
12Ontario Institute of Cancer Research, Toronto, Ontario, Canada
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  • ORCID record for Benjamin Haibe-Kains
Kasper D. Hansen
13Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
14McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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  • ORCID record for Kasper D. Hansen
Hanish Kodali
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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Marie Stephie Louis
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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Arvind Singh Mer
9Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
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Markus Riester
15Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
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  • ORCID record for Markus Riester
Martin Morgan
16Roswell Park Cancer Institute, University of Buffalo, Buffalo, New York, USA
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Vincent Carey
4Harvard TH Chan School of Public Health, Boston, Massachusetts, USA
17Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Levi Waldron
1CUNY School of Public Health, New York, New York, USA
2Institute for Implementation Science in Population Health, City University of New York, New York, USA
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  • ORCID record for Levi Waldron
  • For correspondence: levi.waldron@sph.cuny.edu
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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.

Footnotes

  • The authors declare no potential conflicts of interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted June 01, 2017.
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Software for the integration of multi-omics experiments in Bioconductor
Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez Cabrera, Tiffany Chan, Philip Chapman, Sean Davis, David Gomez-Cabrero, Aedin C. Culhane, Benjamin Haibe-Kains, Kasper D. Hansen, Hanish Kodali, Marie Stephie Louis, Arvind Singh Mer, Markus Riester, Martin Morgan, Vincent Carey, Levi Waldron
bioRxiv 144774; doi: https://doi.org/10.1101/144774
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Software for the integration of multi-omics experiments in Bioconductor
Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez Cabrera, Tiffany Chan, Philip Chapman, Sean Davis, David Gomez-Cabrero, Aedin C. Culhane, Benjamin Haibe-Kains, Kasper D. Hansen, Hanish Kodali, Marie Stephie Louis, Arvind Singh Mer, Markus Riester, Martin Morgan, Vincent Carey, Levi Waldron
bioRxiv 144774; doi: https://doi.org/10.1101/144774

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