R course

Daniel Vaulot

2023-01-17

Installation and reading

Installation

R and R packages

Install the following

• R

• R studio

• Quarto

• VSCode

• the following R packages

# Data manipulation

install.packages("readxl")  # Reading Excel files
install.packages("readr")   # Reading and writing Text files
install.packages("rio")     # Import and export a range of files format
install.packages("dplyr")   # Filter and reformat data frames
install.packages("tidyr")   # Make data "tidy"
install.packages("tibble")  # Manipulate data frames
install.packages("stringr") # Manipulating strings

# Graphics
install.packages("ggplot2")

# Markdown
install.packages("knitr")

# Display tables
install.packages("DT")

Installation

Metabarcoding

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

BiocManager::install("Biobase")
BiocManager::install("Biostrings")
BiocManager::install("dada2")
BiocManager::install("phyloseq")

MetaPR2 package

Two options:

• Interactive web site

• Install as an R package¹

install.packages("devtools")

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

# To run locally the app once installed
metapr2::run_app()

1. You will be asked to install other packages that are required

Data

Please download and unzip on your computer:

• Data for R tutorials

• Metabarcoding dada2 tutorial

Reading material

Session 01-03 - Data analysis

Choose one 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 and Quarto

• Intro to R markdown

Session 05 - Dada2

• Dada2 web site

Session 06 - Phyloseq

• Phyloseq paper
• Phyloseq help - see Tutorials