Supercomputing for Everyone Series (SC4E): Intro to R for Biologists is a Course

### Full course description

The goal of this course, *Supercomputing for Everyone Series (SC4E): Intro to R for Biologists*, is to help biologists get acquainted with R, which will, in turn, help them with their analysis. The course includes five sessions designed to span two weeks. There are no pre-requirements for the course in terms of skills, but some familiarity with Unix is helpful. You can also do the activities on your home computer if you install R yourself.

### Course Module

Chapter 1 - Using and Manipulating Basic R Data Types

- How to Get into R

- R is a Language

- Getting a Bit More Complicated: Vectors

- Vectors of Vectors: Matrices

- Data Frames

- What does the following mean?

- What About Really Complex Data Types

- Get Help

Chapter 2 - R Lab 1: DNA Words

- Install your Packages

- Reading sequence data into R

- QUIZ: Length of a DNA sequence

- QUIZ: Base composition of a DNA sequence

- QUIZ: GC Content of DNA

- QUIZ: DNA words

- Over-represented and under-represented DNA words

- QUIZ: Over-represented and under-represented DNA words

Chapter 3 - Graphing and Making Maps with Your Data

- Graphing Basics

- Mapping Libraries in R

- Mapping Points

- Mapping with Objects

- Using Real Data

- Using Google Satelite Maps

Chapter 4 - R Lab 2: Ordination in R

- Introduction to PCA

- Eigenvalues and Eigenvectors

- A Simple PCA

- QUIZ: A Simple PCA

- QUIZ: Compute the Principal Components

- Compute the Principal Components

- QUIZ: Plotting PCA

- QUIZ: Interpreting the Results

- Graphical Parameters with ggbiplot

- Adding a New Sample

- QUIZ: Project a New Sample onto the Original PCA

- Project a New Sample onto the Original PCA

- A Note on Functions

- Principal Coordinate Analysis

- QUIZ: Distance Calculations

- QUIZ: Computing the Components

- Graphing the PCoA

- QUIZ: Graphing the PCoA

- More on Vegan

- Wrap Up and Back to the Biology

Chapter 5 - Writing Custom Scripts

- Saving and Loading a Script in R

- Best Practices in R - What is a Function?

- Write a function in R

- Blast Summary Function

- Blast Summary Function - Loops

- Blast Summary Function - Some Graphing Functions

- Blast Summary Function - Write to a File

- Blast Summary Function - Final Cleanup

Chapter 6 - R Lab 3: Building a Sliding Window Analysis of GC Content

- Dengue Virus Genome Sequence

- QUIZ: Subsetting Vectors

- Pseudocode

- QUIZ: gcByRange Checkpoint I

- Fill in the code I

- QUIZ: gcByRange Checkpoint II

- Fill in the code II

- Add a Plot I

- QUIZ: gcByRange Checkpoint III

- Add a Plot II

- Just for fun: Overlapping windows

Appendix: R Command Script

- R Commands Script (Chapter 1 & 2)

- R Commands Script (Chapter 3 & 4)

- R Commands Script (Chapter 5 & 6)