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The Jackson Laboratory for Genomic Medicine

Oct 26-27, 2015

9:00 am - 4:00 pm

Instructors: Sheldon McKay, Sue McClatchy, Narayanan Raghupathy

Helpers: Joshy George, Asli Uyar, Zeeshan Ahmed, Francesca Menghi

Please add your name and e-mail address to the waiting list to be contacted when another Software Carpentry session becomes available.

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. This hands-on workshop will cover basic computing concepts and tools including program design, plotting, functions, loops and conditionals. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at all academic levels from undergraduate to senior faculty. No prior programming experience is expected or required. We will create a supportive environment in which instructors and helpers assist with programming exercises and participants help one another. For this reason on-site (rather than remote) participation is required.

Where: 10 Discovery Drive, Farmington, Connecticut. Get directions with OpenStreetMap or Google Maps.

We'll be in rooms 1405 and 1410 located across the hall from the B400 1425 Auditorium.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). If you are using a lab-owned machine please have these installed by IT before the course. IT can install required software quickly and easily, but your instructors will not be able to do so. Participants are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail for more information.


Monday, October 26

09:00 Welcome and introduction to RStudio
09:30 Analyzing patient data
10:30 Coffee/tea break
10:45 Creating functions
12:00 Lunch on your own
13:00 Analyzing multiple data sets
14:30 Coffee/tea break
14:45 Making choices
15:45 Wrap-up

Tuesday, October 27

09:00 Best practices for using R and designing programs
10:30 Coffee/tea break
10:45 Publication quality graphics with R
12:00 Lunch on your own
13:00 Dynamic reports with knitr
14:30 Coffee/tea break
14:45 Making packages in R
15:45 Wrap-up and next steps

Data files: inflammation data.

We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Programming in R

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Reference...


To participate in this Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser. If you are using a lab owned laptop please ask IT to install software for you before the workshop. Your instructors don't have administrative rights to your computer and can't install software for you.


R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.


Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE.

Mac OS X

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.


You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo yum install R). Also, please install the RStudio IDE.