Get started

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:

Use the web interface.

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'))

# Download and install metapr2 in R
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.
Download	Download data for selected samples/taxa as well as the whole dataset as a phyloseq file.
About	Basic information on the metapr2 database.

Citation