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README.md

Tutorials for R

Author : Daniel VAULOT
UMR 7144 CNRS-UPMC, Station Biologique, Place G. Tessier, 29680 Roscoff FRANCE
email: vaulot@sb-roscoff.fr / vaulot@gmail.com

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).

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

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