Technical requirements

The sample data you'll need is available from this book's GitHub repository: https://github.com/danmaclean/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.

The following are the R packages that you'll need. Most of these will install with install.packages(); others are a little more complicated:

• ape
• Bioconductor:
  • Biostrings
  • biomaRt
  • DECIPHER
  • EnsDb.Rnorvegicus.v79
  • kebabs
  • msa
  • org.At.tair.db
  • org.Eck12.db
  • org.Hs.eg.db
  • PFAM.db
  • universalmotif
• bio3d
• dplyr
• e1071
• seqinr

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()

Further information...