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.

Waldron Lab

Waldron Lab Research Website