miaverse – microbiome analytics framework in SummarizedExperiment family

Author(s): Tuomas Borman,Leo M Lahti

Affiliation(s): University of Turku



Because of the complex and high dimensional nature of microbiome profiling data, machine learning and other computational approaches have become an instrumental part of the researcher’s toolkit in this rapidly evolving field. There is an increasing need to develop robust and reproducible methods that take into account current and future trends in microbiome research such as continuously developing methods, multi-omics and expanding datasets. We provide new, enhanced solutions for microbiome data analytics. The emerging analysis framework called miaverse (Microbiome analysis universe) utilizes a standardized data container – TreeSummarizedExperiment – that integrates miaverse to SummarizedExperiment family. We have developed open data science methods particularly designed for microbiome data analysis, visualization, simulation, and time series analysis. Stable versions are available via the Bioconductor network, together with comprehensive online documentation. In addition, the framework has been carefully documented in the Orchestrating Microbiome Analysis (OMA) tutorial book which aims to share the best practices in microbiome research. The miaverse framework addresses the growing need for transparent and reproducible analysis of microbiome data. We anticipate that the framework has the potential to be widely adopted by microbiome researchers, as it is continually evolving to support the latest advancements in the field. This is further facilitated by the tight links to related application domains, such as single cell sequencing, where closely related open source techniques are now being developed.