f3mr: Food Microbiome Metabolic Modules Framework for Taxonomic and Functional Profiling
Résumé
The study of food microbiomes increasingly requires integrative approaches that combine taxonomic and functional perspectives. We present F3MR (Food Microbiome Metabolic Modules in R), a reproducible workflow designed to streamline the analysis of sequencing data from food-associated microbial communities. F3MR enables users to construct tailored reference databases, import raw count data, and aggregate features at multiple taxonomic and functional levels. The resulting count matrices are directly compatible with widely used statistical tools such as DESeq2, facilitating downstream analyses of microbial composition and function. By bridging taxonomy with metabolic modules, F3MR provides a transparent and flexible resource to support reproducible and comparative studies in microbial ecology of food systems.
Domaines
Fait partie de 10.1101/2025.07.31.667869 Autre Tap, J., Mohellibi, N., Tinsley, C., Loux, V., & Chaillou, S. (2025). Food Microbiome Metabolic Modules (F3M), a tool suite for functional profiling of food microbiomes. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.07.31.667869
