Comprehensive Guideline for Microbiome Analysis Using R

Joseph Boctor; Mariam Oweda; Mohamed El-Hadidi

doi:10.1007/978-1-0716-3072-3_20

Comprehensive Guideline for Microbiome Analysis Using R

Methods Mol Biol. 2023:2649:393-436. doi: 10.1007/978-1-0716-3072-3_20.

Authors

Joseph Boctor¹, Mariam Oweda², Mohamed El-Hadidi³

Affiliations

¹ Biotechnology Program, American University in Cairo (AUC), Cairo, Egypt.
² Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, Giza, Egypt.
³ Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, Giza, Egypt. melhadidi@nu.edu.eg.

PMID: 37258874
DOI: 10.1007/978-1-0716-3072-3_20

Abstract

The need for a comprehensive consolidated guide for R packages and tools that are used in microbiome data analysis is significant; thus, we aim to provide a detailed step-by-step dissection of the most used R packages and tools in the field of microbiome data integration and analysis. The guideline aims to be a user-friendly simplification and tutorial on five main packages, namely phyloseq, MegaR, DADA2, Metacoder, and microbiomeExplorer due to their high efficiency and benefit in microbiome data analysis.

Keywords: DADA2; MegaR; Microbiome data analysis; R Packages; microbiomeExplorer; phyloseq.

MeSH terms

Microbiota*
Software