New Results
The tidyomics ecosystem: Enhancing omic data analyses
View ORCID ProfileWJ Hutchison, View ORCID ProfileTJ Keyes, The Tidyomics Consortium, View ORCID ProfileLH Crowell, View ORCID ProfileC Soneson, View ORCID ProfileV Yuan, View ORCID ProfileAA Nahid, View ORCID ProfileW Mu, J Park, ES Davis, View ORCID ProfileM Tang, View ORCID ProfilePP Axisa, View ORCID ProfileN Sato, View ORCID ProfileR Gottardo, M Morgan, View ORCID ProfileS Lee, M Lawrence, View ORCID ProfileSC Hicks, View ORCID ProfileGP Nolan, View ORCID ProfileKL Davis, View ORCID ProfileAT Papenfuss, View ORCID ProfileM Love, View ORCID ProfileS Mangiola
doi: https://doi.org/10.1101/2023.09.10.557072
WJ Hutchison
1Walter and Eliza Hall Institute of Medical Research
2Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
TJ Keyes
3Stanford University School of Medicine, Department of Biomedical Data Science
4Stanford University School of Medicine, Department of Pediatrics
LH Crowell
5University of Zurich, Switzerland
6Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
C Soneson
7Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
8SIB Swiss Institute of Bioinformatics, Basel, Switzerland
V Yuan
9Department of Statistics, The University of British Columbia
AA Nahid
10Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
W Mu
11Biostatistics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
J Park
11Biostatistics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
ES Davis
12Bioinformatics and Computational Biology Program, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
M Tang
13Immunitas Therapeutics
PP Axisa
14Centre de Recherches en Cancerologie de Toulouse, Inserm, Toulouse, France
N Sato
15Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo
R Gottardo
16University of Lausanne
8SIB Swiss Institute of Bioinformatics, Basel, Switzerland
M Morgan
17Roswell Park Comprehensive Cancer Center
S Lee
18Genentech, Department of Bioinformatics and Computational Biology
M Lawrence
18Genentech, Department of Bioinformatics and Computational Biology
SC Hicks
19Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health
20Malone Center for Engineering in Healthcare, Johns Hopkins University, MD, USA
GP Nolan
21Stanford University School of Medicine, Department of Pathology
KL Davis
4Stanford University School of Medicine, Department of Pediatrics
AT Papenfuss
1Walter and Eliza Hall Institute of Medical Research
2Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
M Love
22Genetics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
11Biostatistics Department, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
S Mangiola
1Walter and Eliza Hall Institute of Medical Research
2Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia

Abstract
The exponential growth of omic data presents challenges in data manipulation, analysis, and integration. Addressing these challenges, Bioconductor offers an extensive data analysis platform and community, while R tidy programming offers a standard data organisation and manipulation that has revolutionised data science. Bioconductor and tidy R have mostly remained independent; bridging these two ecosystems would streamline omic analysis, ease learning and encourage cross-disciplinary collaborations. Here, we introduce the tidyomics ecosystem—a suite of interoperable software that brings the vast tidy software ecosystem to omic data analysis.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
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-NC 4.0 International license.
Posted September 13, 2023.
The tidyomics ecosystem: Enhancing omic data analyses
WJ Hutchison, TJ Keyes, The Tidyomics Consortium, LH Crowell, C Soneson, V Yuan, AA Nahid, W Mu, J Park, ES Davis, M Tang, PP Axisa, N Sato, R Gottardo, M Morgan, S Lee, M Lawrence, SC Hicks, GP Nolan, KL Davis, AT Papenfuss, M Love, S Mangiola
bioRxiv 2023.09.10.557072; doi: https://doi.org/10.1101/2023.09.10.557072
The tidyomics ecosystem: Enhancing omic data analyses
WJ Hutchison, TJ Keyes, The Tidyomics Consortium, LH Crowell, C Soneson, V Yuan, AA Nahid, W Mu, J Park, ES Davis, M Tang, PP Axisa, N Sato, R Gottardo, M Morgan, S Lee, M Lawrence, SC Hicks, GP Nolan, KL Davis, AT Papenfuss, M Love, S Mangiola
bioRxiv 2023.09.10.557072; doi: https://doi.org/10.1101/2023.09.10.557072
Subject Area
Subject Areas
- Biochemistry
- Biochemistry (14175)
- Bioengineering (10827)
- Bioinformatics (34316)
- Biophysics (17656)
- Cancer Biology (14758)
- Cell Biology (20784)
- Clinical Trials (138)
- Developmental Biology (11184)
- Ecology (16503)
- Epidemiology (2067)
- Evolutionary Biology (20813)
- Genetics (13677)
- Genomics (19100)
- Immunology (14246)
- Microbiology (33160)
- Molecular Biology (13835)
- Neuroscience (72411)
- Paleontology (542)
- Pathology (2278)
- Pharmacology and Toxicology (3860)
- Physiology (6102)
- Plant Biology (12391)
- Synthetic Biology (3461)
- Systems Biology (8371)
- Zoology (1913)