Skip to main content
SpringerLink
Log in

Comprehensive Guideline for Microbiome Analysis Using R

  • Protocol
  • First Online:
Metagenomic Data Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2649))

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. McMurdie PJ, Holmes S (2013, April 22) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8(4):e61217. https://doi.org/10.1371/journal.pone.0061217

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Dhungel E et al (2021, January 18) MegaR: an interactive R package for rapid sample classification and phenotype prediction using metagenome profiles and machine learning. BMC Bioinform 22(1). https://doi.org/10.1186/s12859-020-03933-4. Accessed 24 Jan 2022

  3. Callahan BJ et al (2016, May 23) DADA2: high-resolution sample inference from illumina amplicon data. Nat Method 13(7):581–583. https://doi.org/10.1038/nmeth.3869. www.nature.com/articles/nmeth.3869

  4. Foster ZSL et al (2017, February 21) Metacoder: an R package for visualization and manipulation of community taxonomic diversity data. PLOS Comp Biol 13(2):e1005404. https://doi.org/10.1371/journal.pcbi.1005404. Accessed 11 Feb 2021

  5. Reeder J et al (2021, June 9) MicrobiomeExplorer: an R package for the analysis and visualization of microbial communities. Bioinform 37(9):1317–1318. https://doi.org/10.1093/bioinformatics/btaa838. http://pubmed.ncbi.nlm.nih.gov/32960962/. Accessed 12 Feb 2022

Download references

Author information

Authors and Affiliations

  1. Biotechnology Program, American University in Cairo (AUC), Cairo, Egypt

    Joseph Boctor

  2. Bioinformatics Group, Center of Informatics Sciences (CIS), Nile University, Giza, Egypt

    Mariam Oweda & Mohamed El-Hadidi

Authors
  1. Joseph Boctor
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mariam Oweda
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mohamed El-Hadidi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mohamed El-Hadidi .

Editor information

Editors and Affiliations

  1. Leeds Institute of Medical Research, University of Leeds, Leeds, UK

    Suparna Mitra

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Boctor, J., Oweda, M., El-Hadidi, M. (2023). Comprehensive Guideline for Microbiome Analysis Using R. In: Mitra, S. (eds) Metagenomic Data Analysis. Methods in Molecular Biology, vol 2649. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3072-3_20

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-3072-3_20

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3071-6

  • Online ISBN: 978-1-0716-3072-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation