Workshop Schedule

Below is the planned schedule for the June 13-15, 2023 Data Lab “Introduction to single-cell RNA-seq” training workshop.

All notebook links contain solutions which we will work through together during the workshop.

Time	Topic
Day 1	2023-06-13
9:00 AM	Slides: Welcome, Introductions and Getting Started (PDF)
10:00 AM	Slides: Introduction to R and RStudio (PDF)
	Notebook: Introduction to R and RStudio
11:15 AM	Coffee break
11:30 AM	Notebook: Introduction to ggplot2
12:30 PM	Lunch
1:30 PM	Notebook: Introduction to tidyverse
2:30 PM	Coffee break
2:45 PM	Exercises and Questions
	Exercise: Introduction to base R
	Exercise: Introduction to R
	Exercise: Introduction to the tidyverse, Part 1
	Exercise: Introduction to the tidyverse, Part 2
3:30 PM	Slides: Introduction to scRNA-seq (pdf)
	Notebook: scRNA-seq quantification
5:00 PM	Adjourn for the day
Day 2	2023-06-14
8:30 AM	Breakfast and coffee
9:00 AM	Questions and Review
9:20 AM	Notebook: scRNA-seq quality control and filtering
10:45 AM	Coffee break
11:00 AM	Notebook: Normalizing scRNA-seq data
12:15 PM	Lunch
1:15 PM	Slides: Dimension reduction and Clustering (pdf)
	Notebook: Dimension reduction with scRNA-seq data
2:30 PM	Coffee break
2:45 PM	Notebook: Clustering and marker gene identification
3:45 PM	Exercises, Questions, and Independent Projects
	Exercise: scRNA-seq quantification
	Exercise: Dimension reduction and clustering
	Resources
5:00 PM	Adjourn for the day
6:00 PM	Dinner at Manayunk Brewery (4120 Main St, Philadelphia, PA 19127)
Day 3	2023-06-15
9:00 AM	Questions and Review
9:30 AM	Slides: Cell type annotation (pdf)
	Notebook: Cell type annotation, Part 1
11:00 AM	Coffee break
11:15 AM	Cell type annotation, Part 2 (Same notebook)
12:30 PM	Lunch
1:30 PM	Exercises, Questions, and Independent Projects
	Exercise: Cell type annotation
	Resources
2:45 PM	Learn about Data Lab scRNA-seq projects
3:00 PM	Participant Presentations!
4:00 PM	Adjourn