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The tidyomics ecosystem: Enhancing omic data analyses

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Hutchison, W. J., Keyes, T. J., Crowell, H. L., Serizay, J., Soneson, C., Davis, E. S., Sato, N., Moses, L., Tarlinton, B., Nahid, A. A., Kosmac, M., Clayssen, Q., Yuan, V., Mu, W., Park, J.-E., Mamede, I., Ryu, M. H., Axisa, P.-P., Paiz, P., Poon, C.-L., Tang, M., Gottardo, R., Morgan, M., Lee, S., Lawrence, M., Hicks, S. C., Nolan, G. P., Davis, K. L., Papenfuss, A. T., Love, M. I. and Mangiola, S. (2024) The tidyomics ecosystem: Enhancing omic data analyses. bioRxiv . 2023.09.10.557072.

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Article Link: https://doi.org/10.1101/2023.09.10.557072

Publisher URL: http://biorxiv.org/content/early/2024/05/22/2023.09.10.557072.abstract

Abstract

The growth of omic data presents evolving challenges in data manipulation, analysis, and integration. Addressing these challenges, Bioconductor1 provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming2 offers a revolutionary standard for data organisation and manipulation. Here, we present the tidyomics software ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning, and encourage cross-disciplinary collaborations. We demonstrate the effectiveness of tidyomics by analysing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas3, spanning six data frameworks and ten analysis tools.Competing Interest StatementR.G. has received consulting income from Takeda and Sanofi, and declares ownership in Ozette Technologies. M.K. is an employee of and declares ownership in Achilles Therapeutics. ​​The remaining authors declare no competing interests.

Item Type:Article
Corporate Creators:Department of Agriculture and Fisheries, Queensland
Business groups:Horticulture and Forestry Science
Subjects:Agriculture > Agriculture (General) > Agricultural economics
Science > Statistics > Statistical data analysis
Agriculture > Agriculture (General) > Farm economics. Farm management. Agricultural mathematics
Agriculture > Agriculture (General) > Agricultural ecology (General)
Live Archive:10 Jun 2024 06:40
Last Modified:10 Jun 2024 06:40

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