Tutorials for R

Author : Daniel VAULOT
UMR 7144 CNRS-UPMC, Station Biologique, Place G. Tessier, 29680 Roscoff FRANCE
email: [email protected] / [email protected]

I have posted here a few tutorials for different types of analysis of microbial communities. For each of these of these tutorials there is a detailed explanation created with Rmd (see below).

• Introduction to R
• Manipulating and plotting data
• Plot data from culture experiments (cell abundance vs. time)
• Visualization and analysis of metabarcode data with phyloseq

Please post any question or issues here : https://github.com/vaulot/R_tutorials/issues

Prerequisites to be installed to run these tutorials

• Download from GitHub the whole set of tutorial

• Unzip the files to a folder on your computer

• Install R

• Install R studio

• Download this set tutorial from GitHub : R tutorials

• Download and install the following libraries by running under R studio the following lines

install.packages("dplyr")     # To manipulate dataframes
install.packages("tidyr")     # To manipulate dataframes
install.packages("readxl")    # To read Excel files into R
install.packages("ggplot2")   # for high quality graphics
install.packages("maps")      # to make maps
install.packages("gridExtra") # for grids
install.packages("treemap")   # for treemaps
install.packages("FactoMineR") # multivariate analysis
install.packages("plotrix" )  # needed for standard error

source("https://bioconductor.org/biocLite.R")
biocLite('phyloseq')          # metabarcode data analysis
biocLite("Biostrings")        # manipulate sequences

Step by step instructions

• Introduction to R
• Manipulating and plotting data
• Plot and process culture data
• Phyloseq analysis of metabarcode data

Feedback

• Please post on GitHub