Easy16S : a user-friendly Shiny web-service for exploration and visualization of microbiome data.

Journées Nutrition et Ecosystèmes Microbiens 2024

Cédric Midoux

PROSE & MaIAGE

April 16, 2024

Metabarcoding workflow

Alvaro (2017)

Exploration and visualisation?

Liu et al. (2020)

Perform Complex Analyses?

  • Depends on huge data, specific formats
  • Requires computational resources
  • Need to install tools locally
  • Training and acquiring expertise in analyses
  • Need time to carry out analyses
  • Integrate data and metadata
  • Tools lack interactivity

We generally use Rscripts but it can be long, complex and requires specific knowledge …

Statement of need

Easy16S is designed to facilitate the exploration, visualization, and analysis of microbiome data !

  • User-friendly interactive web application
  • Convenient functions and default settings
  • To explore, visualize, and analyze metabarcoding data
  • Hosted on an online instance
  • Built with R and based on the phyloseq package
  • Integrated with the FROGS sequence processing suite

Live Demo

Upload data

Transform data

Summary

Tables

Metadata

Barplot

Beta diversity

Differential abundance

Differential abundance

Take Home Messages

Online instance

https://shiny.migale.inrae.fr/app/easy16S

Documentation

https://easy16s.migale.inrae.fr/

GitLab (issues and contributions)

https://forgemia.inra.fr/migale/easy16s

Publication

status

Take Home Messages

Bibliography

NEM research network 2024

Alvaro, Sebastian. 2017. “Amplicon Sequencing and High-Throughput Genotyping – Metagenomics.” http://www.sixthresearcher.com/amplicon-sequencing-and-high-throughput-genotyping-metagenomics/.
Liu, Yong-Xin, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, and Yang Bai. 2020. “A Practical Guide to Amplicon and Metagenomic Analysis of Microbiome Data.” Protein & Cell 12 (5): 315–30. https://doi.org/10.1007/s13238-020-00724-8.