I'm not sure I follow your question.
There are a number of R packages used in the workflow.
Every time you see code, such as
library("Rsamtools"), that is loading an R package called, "Rsamtools". We describe each package used in each respective section, and when there are multiple options, we describe the one we use as well as provide links to alternatives (counting, differential expression analysis, distance calculation, etc.).
You can just search the page here for "library":
And at the end of the page you can see all the libraries which were loaded throughout the R session, under "other attached packages".
Additionally we describe the use of the STAR read aligner in the workflow, with citation and a link to the STAR aligner software. This software is not an R package, but a standalone tool which is run on the command line.