R, Spark, and TextMate
I've been keeping my eye on Spark for a while now, and decided to take the plunge recently after having to do some brief R analyses that were not that complicated and were perfect for Spark. I use TextMate as my R IDE, and I wanted to run my scripts from TextMate right into Spark, and the following are a couple of tips & tricks I found on how to setup everything so that you can start Spark from a command-R (⌘-R) shortcut.
R & Weka
Weka is a great resource for data mining and machine learning. You can get a lot done with the standalone GUI workbench, but sometimes you need to use it as part of a script in a custom R analysis pipeline. Yes, you could create a shell script that makes use of the Weka command-line tools, and invoke said script from R using a 'system' call, but that could get out of hand really quickly.
Circos — Here be Dragons
I have a love/hate relationship with Circos. I love the figures and plots that you can create with it, but I hate having to install it. We have machines that are not upgraded because someone somehow got it working on it, and we are afraid to have to go through the whole process of having to reinstall it. Its awful. Its great.
Backup R Package List
It's the fall holidays, so its time to upgrade my main machine to the latest version of OS X. I should mention that I'm not doing an upgrade, but a clean install of El Capitan. Its a pain in the neck to have to do a clean install, but past upgrade experiences with Lion, Mountan Lion, and Mavericks, have pretty much soured me on "upgrades". No señor. No upgrades.
Life Sciences & Bioinformatics
FSM Stencils
While working on homework for my Theory of Computation class, I found myself in the need for a tool that would allow me to generate Finite State Machine diagrams. I tried Keynote and Power Point, and while they were both good, they weren't great. I was wondering if I should just draw them by hand, when I remembered that OmniGraffle would be perfect for this.
R & TextMate
I love R, and I'm a real ggplot2 nut ... but writing complex programs in the R console, or the built-in editor, has never been my thing. Enter TextMate — its a great editor for writing R scripts in OS X. By using TextMate as your R editor you get a lot of niceties such as syntax highlighting, multiple carets, jump bars for navigating the workspace, code completion, code folding, and much more.