Summary and Schedule
What you will learn
This workshop will introduce R and the tidyverse. The goal is to cover enough to get you started with R, but not for you to become an expert.
We will cover the following topics:
Session 1: Monday 5 December 2022, 1:30pm-5:30pm
- Introduction to R and Rstudio
- Introduction to the tidyverse
- Reading in data with
readrandreadxl - Manipulating data with
tidyranddplyr - Plotting data with
ggplot2
Session 2: Tuesday 6 December 2022, 2:00pm-5:30pm
- Introduction to
bioconductor - Introduction to
Rmarkdown - Version control with
git - Case study: peptide counts during selection
What you will not learn
This course aims to cover a lot of ground quickly. Inevitably, this means things are left out. The goal of this workshop is not to teach you all the details of the material covered, but rather to teach you just enough to get you stared with using R for your work, and where to get help when you need it.
During this course, you should focus on trying to learn the concepts, rather than the details. For example, when we learn about functions, you should not try to memorize all the specific functions that are given as examples, but rather focus on the questions like: What is a function? Why is it useful?
Don’t worry if you don’t understand every detail - you’ll become more comfortable as you start to practice.
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introduction to R and Rstudio |
How do I use the RStudio IDE? What are the basics of R? What are the best practices for writing R code? |
| Duration: 01h 00m | 2. Reading in data |
How can we get data into R?
|
| Duration: 01h 32m | 3. Tidy data |
What is tidy data? How can we pivot data frames to make them tidy? |
| Duration: 01h 54m | 4. Data wrangling |
What are the main dplyr verbs?How can I analyse data within groups? |
| Duration: 03h 01m | 5. Data visualization |
How do you visualize data using ggplot2?How can you combine individual plots? |
| Duration: 04h 03m |
6. Bioconductor and other bioinformatics packages
|
What is bioconductor? What are some bioconductor packages? |
| Duration: 04h 25m |
7. Using R markdown for notebooks and documents
|
How do you write a notebook or document using R Markdown? |
| Duration: 04h 52m |
8. Version control with git
|
What is version control? How to use git in Rstudio? |
| Duration: 05h 04m | 9. Case study |
How do I analyse peptide count data in R?
|
| Duration: 07h 06m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
Data Sets
Download the data zip file.
Software Setup
Ideally you’ll have a laptop to work on during the sessions. If you don’t have a CMRI laptop, you can bring one from home or organise to share with someone that does.