# Basic Concepts of using Phyloseq

The phyloseq package provides many functions for exploring and visualising metagenomics data and we will work through two of the vignettes provided by the package authors today.

A copy of the R source code from the vignettes is available to you in the labs/5_Friday foler, so you can retrace the steps shown in the vignettes.

To find out more about the packge, have a look at the package landing page on the Bioconductor website.

## Set-Up

If we don’t have the appropriate packages intalled yet, we will do so now from the local repository (At home we can just use biocLite to install those).

source("http://192.168.0.9/setRepos.R")
install.packages(c("phyloseq", "metagenomeSeq"))

We can have a look at available vignettes by running the followign command:

vignette(package = "phyloseq")

## Analysis examples

I suggest that we go through the “Phyloseq-Analysis” vignette first, since it allows for a direct “hands-on” exploration of the things we can do with the phyloseq package.

vignette("phyloseq-analysis")

A .pdf copy of the paper correspoding to the GlobalPatterns example dataset is provided in the course materials today, it is referenced in the vignette from time to time and you can use it to compare your plots with the plots from the paper.

## DESeq Example

As a second step we can work through the phyloseq-mixture-models vignette from the phyloseq paper, which will give us an introduction on how to use DESeq2.

vignette("phyloseq-mixture-models")