...
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').
...
In this section session we will use import the abundance table we generated using nfcore/ampliseq in the last session (session 4) into R and then use the ampvis2 package to estimate taxonomic diversity (alpha diversity, beta diversity) , and 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.
...