R Bootcamp for Biolgists

Overview

Introduction to the R programming language with a focus on using it for biological data analysis. The purpose of this course is to teach scientists (students, postdocs, PIs) in the biological and medical sciences to use R for typical data analysis tasks they might encounter routinely. This includes sequence analysis and other bioinformatics tasks. No prior knowledge of R is expected and workshop attendees can expect to come away with a skill set that is immediately translatable to their respective data tasks.

Learning Objectives

At the end of the workshop you will able to:

• Install and update R
• Use the Rstudio IDE
• Understand what CRAN and Bioconductor are and what the differences are between them
• Install and update R packages from CRAN and Bioconductor
• Import a wide variety of data types into R
• Understand the basic data types: integer, numeric, logical, character
• Understand R’s basic data structures: vector, matrix, list, data.frame
• Understand basic programming concepts: functions, objects, loops, vectorization, conditionals
• Manipulate data structures by subsetting and indexing
• Understand key base R functions: seq, apply (and friends)
• Manipulate data with dplyr and friends
• Make plots with ggplot
• Find help about any function
• Understand some common R errors and how to deal with them
• Find and evaluate R packages needed for a particular analysis
• Understand the difference between <- and = and make your own choice about which one to use

Preparation

Attendees are expected to come with their own laptops and have already installed R and RStudio as well as completed at least one of the following online tutorials.

• https://www.datacamp.com/courses/free-introduction-to-r
• http://tryr.codeschool.com/
• http://swirlstats.com/
• http://rforcats.net/

This small bit of preparation will allow us to move quickly through the basics and get to the good stuff.

Course Materials