Introduction to single-cell RNA-seq workshop

Note: Some HBC workshops are taught in person and others are taught online via Zoom. Please take note for scheduling purposes!

Workshop dates and times:

IN-PERSON (Longwood Medical Area):

Tuesday, September 9, 2025: 9:30 AM - 12 PM

Friday, September 12, 2025: 9:30 AM - 12 PM

Tuesday, September 16, 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:

This hands-on workshop will instruct participants on how to design a single-cell RNA-seq experiment, and how to efficiently manage and analyze the data starting from count matrices. This will be a hands-on workshop in which we will focus on using the Seurat package in R.

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:

Introduction to R

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.

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?

Harvard-affiliated researchers who want to learn:

How to design a single-cell RNA-seq experiment
How to use the Seurat package to analyze single-cell RNA-seq count matrices
How to compute and assess QC metrics at every step in the workflow
How to cluster cells based on expression data and derive the identity of the different cell types present
How to combine samples within a dataset, and across datasets using Integration

Cost:

There is a non-refundable and non-transferable $65 registration fee for this advanced workshop.

We will be accepting 25 participants on a first-come, first-served basis:

If you are one of the first 25 eligible* registrants, you will receive an email within 1 week with a link to pay the (non-refundable & non-transferable) $65 registration fee.
If you are not among the first 25 eligible* registrants, you will be added to the waitlist and notified when we open registration for the next iteration of this workshop.

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 three classes.
2-3 hours of reading and exercises from selected lessons before each workshop sessions.
Active participation during discussion sessions.

(Registration opens 2 - 3 weeks before the start of advanced workshops.)

Eligibility:

Preference 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) OR
an AIDS researcher affiliated with Harvard Center for AIDS Research (CFAR).

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.