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Published September 1, 2022 | Version 4.2
Dataset Open

FoodMicrobionet 4.2: mindata files

Creators

  • 1. Parente

Description

This folder contains mindata objects for FoodMicrobionet v4_2. 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

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

Files

mindata_SILVAv138_1.zip

Files (203.1 MB)

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