R for Biologists Workshop
The goal of the workshop is to help biologists get acquainted with R, which will, in turn, help them with their analysis. The workshop includes four sessions designed to span two weeks. There are no pre-requirements for the workshop in terms of skills, but some familiarity with Unix is helpful. The workshop is available on Rstudio, provided through a preconfigured virtual machine hosted on Jetstream. You can also do the activities on your home computer if you install R yourself.
Getting Started on Jetstream
If you would like to use the Jetsteam instance set up for this workshop, simply do an image search for "NCGAS" and click the RStudio Image that pops up. Once the image is up and running, you can copy the IP and add :8787 to the end. For example, if the IP give for my image is 126.96.36.199 the link to RStuido would be 188.8.131.52:8787. Username for all images is guest_user and password is learningR. If you have trouble logging in, try rebooting the image.
Direct link to Jetstream image (TBD)
The goal of this section is to get you acquainted with R, both the environment and the language. We’ll discuss data type manipulation, the structure of commands, how to get help and more information, how to load packages, and how to use the environment. The hope is to make using R more intuitive – the instructors will not be going through a specific analysis or demo. They will focus on reading and make sense of the language (this is very helpful for new users or anyone currently copying, paste, and hoping).
Requirements: There are no requirements for this section, basic Unix (how variables work, cat, pwd, etc.) is helpful as there will be references to bash command similarities, but we won’t be using the command line at all.
The goal of this section is to practice what you learned in the first section. This will be a lab type activity, where you will obtain sequences from NCBI and do some basic analyses.
Requirements: This is a lab based on the material covered in 1, so familiarity with that material is very, very useful (will be posted online after section 1).
The goal of this section is to get a bit more into the depth of how to read, understand, and troubleshoot R code - by introducing classes and functions. Classes and functions are a large part of R, and therefore a large part of understanding the syntax and function of the language. We will also introduce graphing and script creation in R.
Requirements: This material assumes basic usage of R covered in the first section.
The goal of this section is to practice what you learned in the third section. This will be a lab type activity, where you will modify your code from the first lab (second section) to make functions and graphs.
Requirements: This is a lab based on the material covered in section 1 and 3, so familiarity with that material is very very useful (will be posted online after sections). Additionally, this lab builds on the activity from Section 2, but we can provide the starting point for anyone who requests it.
If you have any other questions regarding the workshop, send us an email at firstname.lastname@example.org.