The tidyomics ecosystem: enhancing omic data analyses

• Published in: Nature methods Vol. 21; no. 7; pp. 1166 - 1170
• Main Authors: Hutchison, William J., Keyes, Timothy J., Crowell, Helena L., Serizay, Jacques, Soneson, Charlotte, Davis, Eric S., Sato, Noriaki, Moses, Lambda, Tarlinton, Boyd, Nahid, Abdullah A., Kosmac, Miha, Clayssen, Quentin, Yuan, Victor, Mu, Wancen, Park, Ji-Eun, Mamede, Izabela, Ryu, Min Hyung, Axisa, Pierre-Paul, Paiz, Paulina, Poon, Chi-Lam, Tang, Ming, Gottardo, Raphael, Morgan, Martin, Lee, Stuart, Lawrence, Michael, Hicks, Stephanie C., Nolan, Garry P., Davis, Kara L., Papenfuss, Anthony T., Love, Michael I., Mangiola, Stefano
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.07.2024; Nature Publishing Group
• Subjects: 631/114; 706/648/160; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Brief Communication; Communication; Computational Biology - methods; Data Analysis; Data science; Ecosystems; Ethnicity; Generalized linear models; Genomics; Genomics - methods; Grammar; Humans; Leukocytes (mononuclear); Leukocytes, Mononuclear - cytology; Leukocytes, Mononuclear - metabolism; Life Sciences; Lymphocytes; Peripheral blood mononuclear cells; Proteomics; Science education; Software; Syntax
• ISSN: 1548-7091; 1548-7105; 1548-7105
• DOI: 10.1038/s41592-024-02299-2

The growth of omic data presents evolving challenges in data manipulation, analysis and integration. Addressing these challenges, Bioconductor provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming offers a revolutionary data organization and manipulation standard. 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 analyzing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas, spanning six data frameworks and ten analysis tools. tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.