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HoloFoodR: a statistical programming framework for holo-omics data integration workflows.

Tuomas Borman·Artur Sannikov·Robert D Finn·Morten Tønsberg Limborg·Alexander B Rogers·Varsha Kale·Kati Hanhineva·Leo Lahti
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Abstract

SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10 000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics. AVAILABILITY AND IMPLEMENTATION: HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.

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SoftwareWorkflowAnimalsChickensAlgorithmsSalmonGenomicsComputational BiologyMicrobiotaJournal ArticleResearch Support, Non-U.S. Gov't

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Tuomas Borman, Artur Sannikov, Robert D Finn, Morten Tønsberg Limborg, Alexander B Rogers, Varsha Kale, Kati Hanhineva, Leo Lahti. 2025-11-01. HoloFoodR: a statistical programming framework for holo-omics data integration workflows.. https://doi.org/10.1093/bioinformatics%2Fbtaf605

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