Pseudobulk and related approaches for scRNA-seq analysis
Note: Some HBC workshops are taught in person and others are online via Zoom. Please take note for scheduling purposes!
** ONLINE Workshop dates and times:**
Tuesday, October 21, 2025: 10 AM - 12 PM
Friday, October 24, 2025: 10 AM - 12 PM
Tuesday, October 28, 2025: 10 AM - 12 PM
Friday, October 31, 2025: 10 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.
Who should attend?
Researchers who want to learn:
- How to organize scRNA-seq data for DE analysis
- How to use DESeq2 to obtain a list of differentially expressed genes
- How to visualize expression patterns of differentially expressed genes in single cell RNA-seq data
Cost:
There is a non-refundable and non-transferable registration fee for this advanced workshop*. After registering below, you will receive an email within 1 week with a link to pay.
Priority is given to Harvard Quad and DF/HCC researchers, who are subsidized for this workshop at a price of $65. Others interested in our workshops can find our prices here and should register below.
NOTE: You will not have a reserved seat for this workshop until you pay the registration fee. Please make sure you pay within the time stated in that email, else you will lose your spot to someone on the waitlist.
*NOTE: HMS Graduate Students may receive waivers on registration fees. Please register and we’ll followup with you.
Registration:
Please make sure you take the following into account when signing up for the workshop:
- Mandatory attendance for all four classes.
- 3-5 hours of reading and exercises from selected lessons before each workshop sessions.
- Active participation during discussion sessions.
Eligibility:
Priority is given to Harvard-affiliated researchers:
- at the Harvard Medical School in a lab on the Quad, with grants administered by HMS OR
- at the Harvard School of Dental Medicine, with grants administered by HMS Gordon Hall OR
- an HMS graduate student OR
- affiliated with Dana-Farber / Harvard Cancer Center (DF/HCC)
If you are unsure of your eligibility, please register anyway and we will get back to you.
NOTE: We do not record our training sessions.
Questions?
Please email us at hbctraining@hsph.harvard.edu with any questions.