Single Cell RNA-seq 2023


The course schedule can be found here

Meet your faculty here

Pre-Workshop Materials

Pre-work including programs to install can be found here.

AWS Module

Connecting and properly using a cloud computing cluster at the CBW here

Class Photo

Single Cell RNA-seq Analysis Class of 2023
scRNA23 Workshop Social

Day 1


Nia Hughes

Module 1: Introduction to Single Cell RNA-seq

Trevor Pugh

Module 1 Lecture Slides

Module 2: Read Quantification

Tallulah Andrews

Module 2 Lecture Slides
Lab: Data Structures | Answers | HTML Answers
Lab: Quantification | Answers | HTML Answers

Module 3: Quality Control and Normalization

Tallulah Andrews

Module 3 Lecture Slides
Lab: QC & Normalization | Rmd Answers (first half) | HTML Answers

Day 2

Module 4: Dimensionality Reduction & Visualization

Tallulah Andrews

Module 4 Lecture Slides
Lab: Dimensionality Reduction and Visualization | Answers (second half) | HTML Answers

Module 5: Biological Analyses

Tallulah Andrews

Module 5 Lecture Slides
Lab: Clustering | Answers | HTML Answers

Module 6: Data Set Integration

Gary Bader

Module 6 Lecture Slides
Lab: Data Set Integration | Answers

Post-Workshop Materials


If clicking this link does not start the download, please copy and paste the URL into a new tab or window. Please also note that some of these files are quite large. If you have issues downloading them, contact us at CourseData


We have made our AWS AMI (Amazon Machine Image) publicly available. To launch your own instance, follow the instructions provided by Amazon on how to launch an EC2 instance from a custom Amazon Machine Image. Please note that you will need an AWS account to proceed, and that you will need to upload the CourseData files yourself.

Here are the details of the AMI:

  • AWS Region: us-east-1 (N. Virgina)
  • AMI type: public image
  • AMI name: CBW_scRNA_230719
  • AMI ID: ami-08f9380781016295b

If you want to create and activate a new AWS account, please follow the instructions provided by Amazon.


For information on installing the necessary tools, please visit

Tools Installation