README.md

In erifa1/ExploreMetabar: ExploreMetabar

ExploreMetabar

ExploreMetabar is a shiny application used to explore metabarcoding data (16S, ITS) with interactive plots, integrated statistical tests, and differential analysis.

Online instances

ExploreMetabar is hosted thanks to SK8 INRAE, UCA mesocentre and migale bioinformatics facility:

https://explore-metabar.sk8.inrae.fr

https://shiny.mesocentre.uca.fr/app/exploremetabar

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

Installation

R3.6.3 or upper is required.

• Linux (recommended)

On ubuntu 18.04 those libraries are needed:

apt-get update && apt-get install -y  git-core libcurl4-openssl-dev libgit2-dev libglpk-dev libgmp-dev libicu-dev libpng-dev libssl-dev libxml2-dev make pandoc pandoc-citeproc zlib1g-dev libtiff-dev libjpeg-dev libbz2-dev libgmp3-dev software-properties-common

• Windows

Rtools and git are required.

You can install the development version of ExploreMetabar from this repository with:

install.packages("devtools")
devtools::install_git("https://forgemia.inra.fr/umrf/exploremetabar")

To run Shiny app

library(ExploreMetabar)
ExploreMetabar::run_app()

Docker

To install ExploreMetabar via docker environment:

sudo docker pull erifa1/exploremetabar:latest
sudo docker run -it -p 3838:3838 erifa1/exploremetabar:latest

Citation

Etienne RIFA, & Sebastien Theil. (2020). ExploreMetabar: v1.0.1, https://forgemia.inra.fr/umrf/exploremetabar. Zenodo. https://doi.org/10.5281/zenodo.5245195

erifa1/ExploreMetabar documentation built on Jan. 12, 2023, 1:51 a.m.