Shiny server for the metaPR2 database

An interactive database of eukaryotic metabarcodes compiled from the literature.

Presentation

MetaPR2 is a database of published 18S rRNA metabarcodes. This R package launches a shiny application that allows to interact with the database by mapping, searching and downloading the barcodes.

How run the metaPR2 shiny server

Step 1 - Download the R package

metapr2-shiny

Step 2 - Install package on your computer

• Unpack Zip file

• Launch shiny_metapr2.Rproj

• (Skip this step) If you are running Windows install Rtools

  • https://cran.r-project.org/bin/windows/Rtools/

Step 3 - Install the following libraries

### Shiny
install.packages("shiny" ) 
install.packages("shinyvalidate" ) # For validation of input (easier to use than shinyFeedback)
install.packages("shinycssloaders" ) # For the spinning wheel
install.packages("shinyWidgets" ) # for Extra widgets - https://dreamrs.github.io/shinyWidgets/index.html
install.packages("markdown" ) # To display text boxes in md
install.packages("DT" ) # For table display

### Tidyverse
install.packages("dplyr" )
install.packages("tidyr" )
install.packages("stringr" )
install.packages("forcats" )

### graphics
install.packages("ggplot2" )
install.packages("viridis" )
install.packages("patchwork" )
install.packages("treemapify" )

### maps
install.packages("leaflet" )
install.packages("leaflet.minicharts" ) # To do nice pie charts

### Misc
install.packages("rio" )


### Bioinformatics

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biobase")
BiocManager::install("Biostrings")
BiocManager::install("phyloseq")

Step 4 - Launch the metaPR2 shiny server

Run the following line from R studio

install.packages("pkgload")

pkgload::load_all(".")

metapr2App()

Stop the Shiny application

• Close the browser window

OR

• Hit the stop button at the top right of the bottom left window

In case Shiny application crashes

• Hit the stop button at the top right of the bottom left window
• Relaunch metapr2App()