Introduction to R, specifically aimed at biologists

NCGAS is running a four-part Introduction to R, specifically aimed at biologists.  This workshop is aimed at novices, so if you want to begin learning R or just want to better understand the language, this is a good place to start.  We will be using biological examples, but we won’t be focusing on any one analysis – rather we will focus on how to read the language, how to get help, and where to go next.

 

This is a locally hosted workshop on the Indiana University – Bloomington Campus and takes place over the span of three weeks.  However, if you are interested in following along from afar, material will be posted on our website, and I will have dedicated online “office hours” to help answer questions on the material – even if you are working from a distance.

 

For more information and registering for the on campus course, go HERE.

For online course materials (will be updated when course launches with new materials), go HERE.

For access to online office hours slack (8/28, 8/30, 9/11, 9/13 @ 4 pm EST), go HERE.  Once in slack, go to #life_sciences – that’s where I’ll be at those times!

 

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Supercomputing for Everyone Series: Intro to R for biologists

This is a four-part workshop that will cover the basics of R—the general syntax of the language, the basic data types and how to manipulate them, as well as how to find more information when doing novel analyses. The course does not focus on any particular analysis, but uses DNA sequences as a case study to apply the material covered. We will also cover using Jetstream (the research cloud) to power analyses in RStudio, but use of personal installations on laptops is fine for the workshop. The goal of this course is to get you started in R, so you’ll be able to read and write code, and figure out where to get help when needed.

 

Note: There are four workshops in this series; You must register for the whole series.  If you are unable to attend a specific day, please contact the instructor for material.

 

Objectives: 
By the end of this workshop, users will be able to:

  • Navigate and use RStudio (on and off Jetstream)—load files, export graphs, etc.
  • Understand how to install, load, and use new libraries.
  • Become familiar with Bioconductor Project.
  • Understand basic data types, functions, objects, and classes in R.
  • Write and use a function.

Prerequisites:

  • Unix familiarity is a plus, but not required.
  • A laptop is required—if you do not have one, contact the organizer to borrow one.

Agenda:

  • Day 1:
    The goal of this section is to get you acquainted with R, both the environment and the language. We’ll discuss data types, 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.

    This section does not focus on any individual analysis or demonstration. It focuses on reading and making sense of the language (this is very helpful for new users or anyone currently copying, pasting, and hoping).

    Requirements: There are no requirements for this section. Basic Unix skills (how variables work, cat, pwd, etc.) are helpful, but we won’t be using command line at all, just referencing them throughout.

  • Day 2:
    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 day 1, so familiarity with that material is very, very useful (day 1 material will be available online).

  • Day 3: 
    The goal of this section is to get a bit more in depth on 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.

  • Day 4: 
    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 (day 2) to make functions and graphs.

    RequirementsThis is a lab based on the material covered in days 1 and 3, so familiarity with that material is very, very useful (materials will be posted online after each day). Additionally, this lab builds on the activity from day 2, but we can provide the starting point for anyone who requests it.

This workshop is taught by Research Technologies, a division of University Information Technology Services in conjunction with the National Center for Genome Analysis Support. Both are affiliates of the IU Pervasive Technology Institute.

 

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