Outline

Installation

R and R packages

• Install R

• Install R studio

• Install the following packages

  • Data manipulation
  • readxl : Reading Excel files
  • readr : Reading and writing Text files
  • dplyr : Filter and reformat data frames
  • tidyr : Make data "tidy"
  • tibble : Manipulate data frames
  • stringr : Manipulating strings
  • Graphics
  • ggplot2: Graphics
  • Markdown
  • knitr
  • tinytex
  • Metabarcode analysis
  • phyloseq

Reading material

Session 01-03 - Data analysis

Choose of the two text below. Make sure you make the exercises.

• Statistical Inference via Data Science
  • Chapters 1 to 3

• R for Data Science
  • Chapters 1 to 5
  • Solutions to exercises

Session 04 - Rmarkdown

• Intro to R markdown

Session 05 - Phyloseq

• Phyloseq paper
• Phyloseq help - see Tutorials

Installation - MetaPR2 package

Step 1 - Download the R package

https://daniel-vaulot.fr/html/course-microbes-2021/metapr2-shiny-main.zip

Step 2 - Install package on your computer

• Unpack Zip file

• Launch shiny_metapr2.Rproj

Installation - MetaPR2 package

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" )

Installation - MetaPR2 package

Step 3 - Install the following libraries

### 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")

Installation - MetaPR2 package

Step 4 - Launch the metaPR2 shiny server

Run the following line from R studio

install.packages("pkgload")
pkgload::load_all(".")
metapr2App()

Installation - MetaPR2 package

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()