Introduction to Spatial Transcriptomics

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

ONLINE (Zoom) Workshop dates and times:

Tuesday, May 5, 2026: 10 AM - 12 PM

Friday, May 8, 2026: 10 AM - 12 PM

Tuesday, May 12, 2026: 10 AM - 12 PM

Friday, May 15, 2026: 10 AM - 12 PM

NOTE: Workshop dates are subject to change.

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

Description:

This workshop begins with experimental design considerations and an overview of current spatial transcriptomics technologies. From there, participants will load in Visium HD colorectal cancer samples as a practical example of a spatial analysis workflow. The first half of the workflow will be learning how to load data, assess quality and filter out low-quality bins using Seurat in R. Once the data has been cleaned, a standard single-cell workflow will be used: highly variable gene selection, PCA, UMAP, k-nearest neighbors and clustering. Then, we will apply a deconvolution algorithm to annotate the celltypes in the dataset.

Building upon this foundation, participants will then conduct analyses that incorporate the physical locations of bins on the tissue. This includes spatial clustering, where groups are assigned based upon both gene expression and proximity to neighboring bins in the tissue. Moran’s I will be utilized to identify spatially variable genes, where expression of genes change across different regions of the tissue. The workshop will conclude with a cell-cell communication analysis to assess ligand-receptor interactions between cells that are in close proximity with one another.

Prerequisites:

This is one of our advanced workshops and requires registrants to have a basic fluency in R or attended the following basic workshop offered by our training team in the last 12-24 months:

There is an expectation of participants to have some/all of the following programming knowledge:

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 have attended our Introduction to R workshop (or have working knowledge of R), and want to learn to:

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, HCC researchers and Harvard University CFAR 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 follow-up with you.

Registration:

Please make sure you take the following into account when signing up for the workshop:

  1. Mandatory attendance for all four classes.
  2. 3-5 hours of reading and exercises from selected lessons before each workshop sessions.
  3. Active participation during discussion sessions.
(Please check the eligibility requirements below prior to registering)

Eligibility:

Priority is given to Harvard researchers:

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.