The Jackson Laboratory

June 7-8, 2018

9:00 am - 4:30 pm

Instructors: Vivek Philip, Sue McClatchy, Yuka Takemon

Helpers: Tim Stearns, Stanley Yang, Daniel Alfonsetti, Duy Pham, Andrew Deighan

General Information

Where: Bioinformatics Training Room 1540, 600 Main Street, Bar Harbor, ME. JAX employees can locate the bioinformatics training room in building 1, unit 5 on this campus map. Visitors should bring photo ID and meet at the visitor entrance by 8:30am. Get directions with OpenStreetMap or Google Maps.

When: June 7-8, 2018. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email for more information.


Thursday, June 7

09:00 Workshop Overview
09:15 Introduction to R and RStudio
10:15 Project Management With RStudio
10:30 Seeking Help
10:45 Coffee
11:00 Producing Reports With knitr
12:00 Lunch break
13:00 Dataframe Manipulation with dplyr
14:30 Coffee
14:45 Dataframe Manipulation with tidyr
16:15 Wrap-up

Friday, June 8

09:00 Creating Publication-Quality Graphics
10:15 Vectorization
10:45 Coffee
11:00 Control Flow
12:00 Lunch break
13:00 Functions Explained
14:30 Coffee
14:45 Writing Data
16:15 Wrap-up

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


Programming in R


To participate in a workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.


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


Video Tutorial

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.


Video Tutorial

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 dnf install R). Also, please install the RStudio IDE.