easy16S

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

The goal of easy16S is to provide a user-friendly interactive web-application with convenient functions and default settings to explore, visualize and analyze metabarcoding data.

It builds upon the phyloseq package and its extensions and is tightly integrated with the FROGS sequence processing suite.

Easy16S can be accessed directly via an online instance: https://shiny.migale.inrae.fr/app/easy16S.

Installation

You can install the development version of easy16S like so:

# install.packages("remotes")
remotes::install_gitlab(
  repo = "migale/easy16S@main",
  host = "forgemia.inra.fr"
)

Run the Shiny Application

To run the Shiny application, execute the following code in your R environment:

easy16S::run_app()
easy16S::run_app(physeq = phyloseq.extended::food) # directly load your data

Docker Integration

For each release, a CI/CD pipeline builds a Docker image using a Dockerfile. This process is particularly useful for deploying with ShinyProxy.

The Docker images are available in the container registry.

The image exposes port 3838 and launches the app using easy16S::run_app(options = list(launch.browser = FALSE))

Therefore, to run the application, execute the following commands:

docker pull registry.forgemia.inra.fr/migale/easy16s:v24.03
docker run --rm --publish 3838:3838 registry.forgemia.inra.fr/migale/easy16s:v24.03

The app will be accessible at http://localhost:3838/.

Issues and Support

If you encounter any bugs or have suggestions for improvement, please use the issue tracker.

Cite us

We appreciate acknowledgment from research teams using Easy16S. Please include the following sentence in the publications of your analyses: “We are grateful to the INRAE MIGALE bioinformatics facility (MIGALE, INRAE, 2020. Migale bioinformatics Facility, doi: 10.15454/1.5572390655343293E12) for providing help and computing resources”.

A scientific publication related to Easy16S is currently in preparation.

Code of Conduct

Please note that the easy16S project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.