This tutorial will go over a basic analysis workflow using HMP data kindly provided in phyloseq format by Paul J. McMurdie
Download the data here

For pre-processing your own data, I recommend following this DADA2 tutorial.

If you need help getting your own data into phyloseq format, see phyloseq data import tutorials.

The R package “phyloseq” is designed specifically for analysing microbiome data. For more information, see the home page. A phyloseq object holds all of the data necessary for the analysis in a single place. It can contain: metadata for the samples, the abundance table, taxonomic assignments, a phylogenetic tree, and reference sequences. See the schematic below for how these data are linked together in a phyloseq object.