The analysis scripts in this guide are written in R script. We will be using RStudio, a front-end gui for R, to run the analysis scripts.
The key R analysis package we’ll be using is ampvis2 ('Tools for visualising amplicon data').
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In this session we will import the abundance table we generated using nfcore/ampliseq (session 4) into R and then use the ampvis2 package to estimate taxonomic diversity (alpha diversity, beta diversity) and bacterial community structure.
For this workshop we will be using rVDI virtual desktop machines, which run on the HPC.
This is to save setup time, because installing R and all the required analysis packages would take over an hour.
If you want to run the analysis at home, without using rVDI, you can install R and RStudio on your PC.
Installing R: The rVDI virtual machines already have all of this installed.
Here’s an example report containing many of the analyses we’ll be running today:
https://crandata.r-project.org/Installing RStudio: RStudio Desktop eresearchqut.net/paulw/public/Mahsa_man2_final/index.html