Microbiome Helper 2 Importing data into R - LangilleLab/microbiome_helper GitHub Wiki

Authors: Robyn Wright
Modifications by: NA
Based on initial versions by: NA

The aim of this page is to give an overview of importing any of the final exports that we've created from the other workflows into R, so that we'll be able to run some of the other analyses on them. First off, if you aren't already familiar with RStudio and R notebooks, I'd recommend reading through that page.

We'll continue adding to this page with the output of the different tutorials, but the main aim is to get everything into a Phyloseq object so that we'll be able to use this for downstream analyses, so you won't need to run through everything on this page, just the parts that are relevant for you.

We'll assume that for the most part, you will be adding these bit of code to an R notebook and running the chunks from there.

Install packages

Load required packages and setup