Many bioinformatic resources must be run from the command line, also referred to as the shell or terminal. “*nix” refers to Linux/Unix, but a terminal can also be used from OSX and even Windows.
Regular Expressions (regexes) are included here even though they are widely useful in R and other programming languages for powerful string matching.
- Software Carpentry - very nice self-guided tutorials on the essentials of the command line. This is a good starting point.
- RegExr - Great site for beginners to practice regexes, and experts to build complicated regexes. It lets you build and see the results of your expression instantly, with help on the side-bar.