The metaPR2 shiny application allowing access to the metaPR2 database is provided as a R package called metaPR2. This page provides instruction to install and use the package.

You can also:

## Installation

Install from the GitHub web site using the devtools package

install.packages(devtools)
devtools::install_github("pr2database/metapr2-shiny")

Alternatively you can also install from R-universe

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

install.packages('metapr2')

## Run the Shiny application

metapr2::run_app()

#### Stop and relaunch the Shiny application

• Hit the Disconnect button at the top of left panel.

#### In case Shiny application crashes

• Hit the Disconnect button at the top of left panel.
• Relaunch run_app()

## Structure of the application

panel/subpanel content
Datasets Select and list datasets used. You can select also groups of datasets (e.g. arctic)
Taxonomy List the taxa present in the metaPR2 database and the number of ASVs for each
Treemap Create treemaps (square pie-chart) provinding the proportion of each taxon for the samples and datasets selected
Map Maps of read abundance. For a given taxonomic level you can visualize the proportions of the taxonomic levels below (e.g. species if you are at the genus level) or alternatively the main taxon at each station (e.g. the mainn species if you are the genus level). Size of circle is proportional to contribution of taxon to total eukaryotes.
Barplot Composition for specific variables (e.g. depth_level).
Diversity Diversity analysis using the R phyloseq package
- Alpha diversity Alpha diversity indices (e.g. Shannon, Simpson).
- Beta diversity Mutivariate analyses (e.g. NMDS).
Query Enter a sequence and search for metabarcode that are similar to your sequence using a BLAST like search. You can plot the ASVs matching your query.
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