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

Rencontres R 2024

Cédric Midoux

PROSE & MaIAGE

June 13, 2024

Metabarcoding (16S) workflow

Exploration and visualization?


With R?

⇒ Hard to master


Users need an interactive and user-friendly tool!

Let me introduce {easy16S}

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

  • User-friendly interactive web application with Shiny
  • Explore, visualize, and analyze metabarcoding data
  • Built with R and based on the phyloseq package
  • Convenient functions and default settings

Behind the scenes

  • Built like a package with golem
  • Hosted online on the MIGALE instance of shinyproxy
  • Containerized with Docker, CI/CD deployed with .gitlab-ci.yml in a renv reproducible environment
  • Documented with pkgdown pages
  • Licensed under GNU AGPLv3

Live Demo

Interface

Metadata (with esquisse)

Compositional Barplots

Beta Diversity Visualization

Differential Abundance

Use-Case

  • Beginner users: Autonomous analyses without any technical skills
  • Advanced users: Swiftly explore data and identify patterns
  • Training sessions: Focus on biological concepts without being limited by programming challenges

Publication: status

Take Home Message

Thank you for your attention


Cédric Midoux

cedric.midoux@inrae.fr

Bibliography

Rencontres R 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.