There are a number of text conventions used throughout this book.

CodeInText: Indicates code words in text, database table names, folder names, filenames, file extensions, pathnames, dummy URLs, user input, and Twitter handles. Here is an example: "We'll look at using the ape and treeio packages to get tree data into and out of R. "

A block of code is set as follows:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")
BiocManager::install()

Bold: Indicates a new term, an important word, or words that you see on screen. For example, words in menus or dialog boxes appear in the text like this. Here is an example: "Some of the dependencies rely on encapsulated Java code, so you'll need to install a Java Runtime Environment (JRE) for your system."