Introduction to single-cell RNA-seq workshop (Python-based)

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

ONLINE (Zoom) Workshop dates and times:

Tuesday, August 11, 2026: 9:30 AM - 12 PM

Friday, August 14, 2026: 9:30 AM - 12 PM

Tuesday, August 18, 2026: 9:30 AM - 12 PM

Friday, August 21, 2026: 9:30 AM - 12 PM

Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!

Description:

This hands-on workshop will cover best practices for designing and analyzing single-cell RNA-seq experiments using the Scanpy package in Python. Starting from a raw counts matrix, we will work directly in Python to complete a standard analysis.

The beginning of the workflow will address what quality control metrics should be used to identify high quality cells in a dataset. After this cleaning step, we will follow a standard single-cell workflow, including normalization and integrating disparate datasets. This will give the foundation for us to identify cells that are similar to one another with PCA, UMAP, and clustering algorithms. Finally, using statistical tests to identify unique genes in each cluster, we will get to ultimate end goal of this workshop - annotating the celltypes in the dataset.

By the end of the workshop you will have analyzed a single-cell RNA-seq data from loading in the raw data to producing annotated celltypes - all within Python!

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 Python

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 Python.
Ability to use functions regularly and can modify arguments when necessary.
Comfortable installing libraries and troubleshooting issues.
Data wrangling expertise (subsetting vectors and data frames) using Pandas
Familiarity with Seaborn for data visualization.

I am fluent in Python but have not attended the HBC prerequisite workshop, can I still register?

Yes, please register and provide your Python/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 Scanpy 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 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, DF/HCC and Harvard University CFAR 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.

(Please check the eligibility requirements below prior to registering)

Priority:

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

NOTE: We do not record our training sessions.

Questions?

Please email us at hbctraining@hsph.harvard.edu with any questions.