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

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

Jan 1 - Jan 1, 2020


Full course description

The goal of this course 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)

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