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

Cédric Midoux

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## To cite this version:

Cédric Midoux. Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.. Symposium FROGSdays, INRAE, Dec 2025, Toulouse, France. hal-05393313

HAL Id: hal-05393313

https://hal.inrae.fr/hal-05393313v1

Submitted on 2 Dec 2025

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Distributed under a Creative Commons Attribution - ShareAlike 4.0 International License
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# Easy16S: a user-friendly Shiny web-service for exploration and visualization of microbiome data.

## Symposium FROGSdays

Cédric Midoux ID

PROSE & MAIAGE

December 3, 2025

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hal-05393313

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This work is licensed under a Creative Commons Attribution-ShareAlike 2.0 Generic License.
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# Metabarcoding (16S) workflow

1

Collect an
environmental
sample

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2

DNA extraction
from environmental
sample

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3

Amplify DNA
markers

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4

High-throughput
sequencing

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5

Bioinformatic
processing

6

Species
identification

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7

Ecological
analysis

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# Exploration and visualization?

## With R?

⇒ Hard to master

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spend
time
mastering R

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call
your favourite
bioinformatician

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# 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 (McMurdie and Holmes 2013)

* Convenient functions and default settings
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Live Demo

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Upload Data

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# Transform Data

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# Summary

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# Tables

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# Metadata (with esquisse)

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# Compositional Barplots

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# Beta Diversity Visualization

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# Differential Abundance Analysis

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# Differential Abundance Analysis

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# Use Cases

* Beginner users 🐣: Autonomous analyses with no technical hurdles

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* Advanced users 🐶: Swiftly explore data and identify interesting patterns for further exploration

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* Training sessions 🎓: Focus on exposing biological concepts without wasting time on missing commas

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# Deliverables

* 📦 ShinyApp in a R package

* {golem} framework

* GNU AGPLv3 licence

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* ⚢ GitLab repository

* migale/easy16s

* Issues and contributions

* Archived in HAL hal-04304559 and SWH archived release v24.07

* 📑 Documentation (built with {pkgdown}

* easy16s.migale.inrae.fr

* 🐢 Docker image (built with CI/CD)

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* registry.forge.inrae.fr/migal

* renv for reproducible environment

* 🌐 Online ShinyProxy instance

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* shiny.migale.inrae.fr/app/easy16S
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JSS

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JSS

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JSS
The Journal of Open Source Software

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

Cédric Midoux 1,2,3, Olivier Rué 2,3, Olivier Chapleur 1, Ariane Bize 1,
Valentin Loux 2,3, and Mahendra Mariadassou 2,3

1 Université Paris-Saclay, INRAE, PROSE, 92761, Antony, France 2 Université Paris-Saclay, INRAE, MalAGE, 78350, Jouy-en-Josas, France 3 Université Paris-Saclay, INRAE, BioinfOmics, MIGALE bioinformatics facility, 78350, Jouy-en-Josas, France

DOI: 10.21105/joss.06704

Software

• Review ↗

• Repository ↗

• Archive ↗

Summary

The analysis of microbiome data has become a major asset for investigating microbial diversity and dynamics, in diverse fields, like health (Chatelier et al., 2013), environmental studies (Karimi et al., 2020), food-processing (Chaillou et al., 2014), or environmental biotechnologies

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Thank you for your attention

Cédric Midoux

cedric.midoux@inrae.fr

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Bibliography

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.

McMurdie, Paul J., and Susan Holmes. 2013. "Phyloseq: An r Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data" 8 (April): e61217. https://doi.org/10.1371/journal.pone.0061217.

Midoux, Cédric, Olivier Rué, Olivier Chapleur, Ariane Bize, Valentin Loux, and Mahendra Mariadassou. 2024. "Easy16S: A User-Friendly Shiny Web-Service for Exploration and Visualization of Microbiome Data." *Journal of Open Source Software* 9 (103): 6704. https://doi.org/10.21105/joss.06704.