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
-
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
- Introduction to R
- Manipulating and plotting data
- Plot and process culture data
- Phyloseq analysis of metabarcode data
- Please post on GitHub