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.
In this section we will use the abundance table we generated using nfcore/ampliseq in the last session to estimate taxonomic diversity (alpha diversity, beta diversity), bacterial community structure and infer gene expression. Details of this analysis are in those sections of this analysis workflow.
The key R analysis package we’ll be using is ampvis2 ('Tools for visualising amplicon data').
The final section of the workflow examines differential abundance of taxa between sample groups. The main R package used in this analysis is AMCOM-BC: https://bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC.html
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. The rVDI virtual machines already have all of this installed.