metaPR2

A database of 18S rRNA metabarcodes

Version: 2.1.0 - 59 datasets

Release date: 2023-05-16

Presentation

MetaPR2 is a database of published 18S rRNA metabarcodes that have been reprocessed and assigned using PR2.

Acessing the database

Access to the database to map, search and download the barcodes can be done in three different ways:

• Using a web interface.

• Download the R package and launch the shiny application.

1 - Web interface

• Launch in your browser: http://shiny.metapr2.org
• Help : https://pr2database.github.io/metapr2-shiny/articles/

2 - metaPR2 shiny R package

Install the package from GitHub

install.packages(devtools)

devtools::install_github("pr2database/metapr2-shiny")

Note: You may have to install some packages required by metapr2 if they are not installed on your machine

Alternatively install from R-universe

No need in this case to install package devtools

# Enable repository from pr2database
options(repos = c(
  pr2database = 'https://pr2database.r-universe.dev',
  CRAN = 'https://cloud.r-project.org'))

# Download and install metapr2 in R
install.packages('metapr2')

Launch shiny interface with function run_app()

metapr2::run_app()

Help

Extensive help is provided here.

Errors

Please report errors in the Issues page of the metaPR2 database.

Citation

Vaulot, D., Sim, C.W.H., Ong, D., Teo, B., Biwer, C., Jamy, M., Lopes dos Santos, A., 2022. metaPR$^{2}$: a database of eukaryotic 18S rRNA metabarcodes with an emphasis on protists. Molecular Ecology Resources 22, 3188–3201. https://doi.org/10.1111/1755-0998.13674

Resources

• Website: https://shiny.metapr2.org/

• Source code: https://github.com/pr2database/metapr2-shiny

• Docker (only version <= 1.0.2): https://hub.docker.com/repository/docker/vaulot/metapr2

Maintainer

• Daniel Vaulot: [email protected]

Contributors

• Daniel Vaulot, CNRS Roscoff, NTU-ASE Geek lab
• Adriana Lopes dos Santos, NTU-ASE Geek lab
• Clarence Sim, NTU-ASE Geek lab
• Denise Ong, NTU-ASE Geek lab
• Bryan Teo, NTU-ASE Geek lab
• Charlie Biwer, Uppsala University Sweden
• Mahwash Jamy, Uppsala University Sweden