R course
Daniel Vaulot
2023-01-17
Installation and reading
Installation
R and R packages
Install the following
# 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
MetaPR2 package
Two options:
Install as an R package1
Data
Please download and unzip on your computer:
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
Session 05 - Dada2
Session 06 - Phyloseq
- Phyloseq paper
- Phyloseq help - see Tutorials
R course Daniel Vaulot 2023-01-17 Installation and reading