Orchestrating microbiome multi-omics with R/Bioconductor

Author(s): Leo M Lahti,Tuomas Borman,Sudarshan A Shetty

Affiliation(s): Department of Computing, University of Turku, Finland

Social media: https://twitter.com/antagomir

A number of R/Bioconductor packages for microbiome data science have been released in the recent years. The majority of the existing frameworks and packages focus on the analysis of taxonomic profiling data generated by phylogenetic microarrays, 16S amplicon sequencing, or metagenome analysis. However, there is an increasing need to integrate taxonomic profiles with other measurement types, such as transcriptomics, metabolomics, host genomics, cross-kingdom analysis, and hierarchical side information of the features and samples. Modern data containers, such as the MultiAssayExperiment, have opened up new opportunities for developing a systematic approach to multi-table data integration in microbiome studies. A dedicated ecosystem of tools for microbiome analysis can provide valuable, targeted tools for those focusing on microbiome and metagenome profiling data sets. We will discuss recent advances in microbiome data integration and the associated package ecosystem in R/Bioconductor, highlighting links to related work in other areas such as transcriptomics and single-cell studies that are greatly accelerating these community-driven efforts.