The Jackson Laboratory

Mar 15-16, 2018

9:00 am - 4:30 pm

Instructors: Yuka Takemon, Georgi Kolishovski, Narayanan Raghupathy

Helpers: Sue McClatchy

General Information

Where: Bioinformatics Training Room 1540, 600 Main Street, Bar Harbor, Maine. Get directions with OpenStreetMap or Google Maps. JAX employees can locate the bioinformatics training room in building 1, unit 5 on this campus map.

When: Mar 15-16, 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 organisers 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 susan.mcclatchy@jax.org for more information.


Schedule

Thursday, March 15

09:00 Workshop Overview
09:15 Introduction to R and RStudio
10:15 Project Management With RStudio
10:30 Seeking Help
10:35 Understanding the File System
10:45 Coffee
11:00 Producing Reports With knitr
12:00 Lunch break
13:00 Control Flow
14:30 Coffee
14:45 Creating Publication-Quality Graphics
16:15 Wrap-up

Friday, March 16

09:00 Vectorization
09:45 Functions Explained
10:45 Coffee
11:00 Dataframe Manipulation with dplyr
12:00 Lunch break
13:00 Dataframe Manipulation with dplyr (continued)
13:30 Dataframe Manipulation with tidyr
14:30 Coffee
14:45 Ggplot with knitr
15:45 Writing Data
16:15 Wrap-up

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


Syllabus

Programming in R



Setup

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

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

Windows

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.

Mac OS X

Video Tutorial

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

Linux

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.