FoodMicrobionet 4.2: mindata files

This folder contains mindata objects for FoodMicrobionet v4.2.1. These objects allow, via the NCBI accession number, direct access to information on individual studies. Each object is a R list containing:

• Study_accn = the study accession number,
• study_df = a data frame with the study information,
• overlap = a logical flag indicating if overlapping paired sequences were used,
• pend = a logical flag indicating if paired sequences were used,
• physeq = a phyloseq object with sample, taxa, OTU tables and, when available, a phylogenetic tree,
• rev_compl = a flag indicating if the sequences need to be transformed in reverse complement before taxonomic assignment

This project is currently co-funded by Ministero dell'Università e della Ricerca PRIN 2022, proposal 2022NN28ZZ, and received funding from the European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR)) CUP C53D23005460006

Refer to this publication for further detail on v4.1 of FoodMicrobionet:

Parente, E., Zotta, T., Ricciardi, A., 2022. FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities. Int J Food Microbiol 372, 109696. https://doi.org/10.1016/j.ijfoodmicro.2022.109696