There’s many pieces of software I use on a daily basis, along with some I use less frequently. In this post, I’m just going to list some of these out, but in subsequent posts, I’ll go into a little more detail about what I use and why, as well as how I structure my projects.

This list is in no particular order:

  • R (
    • My statistical package of choice. R has a great community, there are many resources for beginner’s, and those more advanced, and it’s open source and free!
  • emacs (
    • I prefer to write everything in a text editor. I’ll go into detail in a later post, and try and remember to link to it from here. I’m not interested in an emacs vs. vi/vim war. You can read about that all over the interwebs (it has a wiki page too)
  • git/GitHub ( and
    • Distributed version control. Keep your source files synced across computers/systems. Git is the version control system, and github is an online repository for your files. This blog is hosted on GitHub.
  • pandoc (
    • As stated on its about page, pandoc is ‘… your swiss-army knife’. You can use pandoc to convert between different markup formats. As an example, this post is written in markdown, but using pandoc, I could easily convert it to a Word document with a single commandline command.
  • Excel (
    • I really don’t need to say anything, or link to it, but I’ve done it for the others, so let’s be fair! Spreadsheets are a great way of getting a quick overview of your data (after it has been collected), but leaving the analysis and graphical displays to better tools (R, stata, etc.)
  • REDCap (
    • We use REDCap at our institution for data management, and I use it personally to track my projects. It’s an easy to use web-based application for creating and managing databases for surveys and research. It’s free, but you (your institution) need to join the REDCap consortium as a partner to get the code

I use other software as well, and also use the mighty pen-and-paper system as well, but I’ll discuss those in later posts, if and when I need to.