Data Lab Training Modules

This repository is a collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.

If you are a childhood cancer researcher and are interested attending a workshop go to the Data Lab's website to learn more about our upcoming workshop locations and dates.

Here is a sample schedule for the RNA-seq workshop if you'd like to see the order in which this material is presented. The data files that we process in the course are too large to be stored on GitHub so you will not be able to follow the material exactly as written without attending a workshop.

Structure of each module:

Background slides:

The accompanying slides for each module are linked below and briefly introduce the concepts underlying each module.

• Intro to RStudio
• RNA-seq
• Machine learning
• Intro to scRNA-seq
  • Intro to scRNA-seq
  • Dimensionality reduction and Clustering
  • Cell type annotation
• Advanced scRNA-seq
  • scRNA-seq refresher
  • Integration
  • Differential expression
  • Intro to Pathway Analysis

Cheatsheets:

Cheatsheets for each module are named and linked below. Each cheatsheet consists of functions that are used in its corresponding module, along with links to documentation on the usage of these functions.

These cheatsheets can also be found in the folder named module-cheatsheets.

• Intro to R tidyverse cheatsheet
• RNA seq cheatsheet
• scRNA-seq cheatsheet
• Advanced scRNA-seq cheatsheet
• Converting to/from SCE objects cheatsheet
• Pathway analysis cheatsheet
• Machine learning cheatsheet