setup: Set up environment to use 'amplicR'
In carlopacioni/amplicR: An R package to process amplicon data

setup

R Documentation

Set up environment to use `amplicR`

Description

Install/update additional packages needed that are not installed the conventional way.

Usage

setup()

Details

Bioconductor recommends installing its packages using

source("https://bioconductor.org/biocLite.R")

and

biocLite().

This is what I do, but this also implies that amplicR's dependencies are not installed when amplicR is installed. To circumvent this issue, this function will check whether Bioconductor is installed and whether its packages need to be updated. Also, because dada2 is not currently available from CRAN nor from Bioconductor, it is installed by this function via devtools. If you have installed or want to install these packages manually, you don't have to use this function. If you do run this function, make sure that you do so when you first load amplicR (i.e. a fresh R session) so that no Bioconductor's packages are in use and it is possible to update them if needed.