The sample data you'll need is available from this book's GitHub repository at https://github.com/PacktPublishing/R-Bioinformatics-Cookbook. If you want to use the code examples as they are written, then you will need to make sure that this data is in a sub-directory of whatever your working directory is.
Here are the R packages that you'll need. Most of these will install with install.packages(); others are a little more complicated:
- ape
- Bioconductor
- dada2
- phyloseq
- corrplot
- cowplot
- dplyr
- kmer
- magrittr
- metacoder
- RColorBrewer
- vegan
Bioconductor is huge and has its own installation manager. You can install it with the following code:
if (!requireNamespace("BiocManager")) install.packages("BiocManager") BiocManager::install()