Set up

Software

REQUIRED - We will be using RStudio to analyse the data set. It is recommend you have the following installed: RStudio version 1.4 or later and R version 4.0 or later. Further details on getting started in RStudio here.

Optional (not needed for today’s workshop) - We will not be doing the sequence processing steps today but if you did want to do this you will need to download conda and QIIME2.

Download data

Raw Sequence data (optional)

The input for analysis is raw sequence data in .fastq format. Zipped files come in the format .fastq.gz

Rename so fastq.gz files are in the format SAMPLEID_INITIALS_LIBRARYID_L001_R1_001.fastq.gz (forward) or SAMPLEID_INITIALS_LIBRARYID_L001_R2_001.fastq.gz (reverse).

The raw sequence data can be downloaded from repository link here.

RData (REQUIRED)

The easiest way to follow along with this tutorial is to download this GitHub repository using either option A or B below:

OPTION A. Go to https://github.com/siobhon-egan/BIO510-microbiome and click on the green Code button. Select Download ZIP, open/unzip the file. Open the .Rproj file which should automatically open a project in RStudio.

OPTION B. Use terminal and clone the GitHub repo.

git clone https://github.com/siobhon-egan/BIO510-microbiome.git

Install R packages

You should only need to do this once to install required libraries.

I recommend you run this bit of code line by line.
As there are dependencies between packages it is best to run them in the order outlines below.

Remember it assumes you have R version 4.0 and RStudio version 1.4.

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
# Phyloseq
BiocManager::install("phyloseq")
# Tidyverse
install.packages("tidyverse")
# Install microbiome utilities
install.packages("devtools")
devtools::install_github("microsud/microbiomeutilities")
# Install MicrobiotaProcess
BiocManager::install("MicrobiotaProcess")
# Install ampvis2
install.packages("remotes")
remotes::install_github("MadsAlbertsen/ampvis2")
# Install vegan
install.packages("vegan")
# Install ggpubr
install.packages("ggpubr")
# R color brewer
install.packages("RColorBrewer")
# agricolae
install.packages("agricolae")
# viridis
install.packages("viridis")
# ape
install.packages("ape")
# DESeq2
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("DESeq2")

Note I have not included packages that relating to “knitting” the document here. Everything should be executable within the R markdown files by running the code chunks.