Pseudobulk and related approaches for scRNA-seq analysis
Date and Time
Location
** Workshop dates and times:**
IN-PERSON (Longwood Medical Area):
Tuesday, October 21, 2025: 9:30 AM - 12 PM
Friday, October 24, 2025: 9:30 AM - 12 PM
Tuesday, October 28, 2025: 9:30 AM - 12 PM
Friday, October 31, 2025: 9:30 AM - 12 PM
NOTE: Workshop dates are subject to change - please check back
Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!
Description:
After clustering cells as part of a single-cell RNA-seq experiment, investigators are often interested in carrying out a differential expression analysis between conditions within certain cell types. When the experimental design includes replicates with multi-conditions there is power in identifying differentially expressed genes using a pseudbulk approach. In this hands-on workshop, we will:
- Discuss various approaches for differential expression using single cell RNA-seq data
- Prepare single-cell RNA-seq raw count data for pseudobulk analysis
- Perform differential expression analysis on pseudobulk counts using DESeq2
- Present approaches for evaluating differential proportions of cells between conditions
Prerequisites:
This is one of our advanced workshops, and requires registrants to have attended the following Basic workshop offered by our training team in the last 6-8 months:
There is an expectation of participants to have some/all of the following programming knowledge:
- Solid understanding of data structures and fluent implementation of basic syntax in R.
- Ability to use functions regularly and can modify arguments when necessary.
- Comfortable installing packages and troubleshooting issues.
- Data wrangling expertise (subsetting vectors and data frames) using base R or tidyverse
- Familiarity with ggplot2 for data visualization.
- Familiarity with RStudio interface
Participants in this workshop would benefit from having some familiarity with single-cell RNA-seq analysis and the use of the R Seurat package, but it is not a requirement.
I am fluent in R but have not attended the HBC prerequisite workshop, can I still register?
Yes, please register and provide your R/programming exerience on the form, and we’ll get back to you.