Author: Jason Shapiro, Ph.D.
| # | Tutorial | Description |
|---|---|---|
| 01 | Visium: Preprocessing | Loading Visium data, QC, normalization, dimensionality reduction, spatially variable gene detection, and integration with a single-cell reference |
| 02 | Visium: Spatial Clustering | Spatial clustering with BayesSpace, BASS, and MEcell |
| 03 | Visium: Deconvolution | Cell type deconvolution using Seurat label transfer and RCTD |
| 04 | Visium: Cell-Cell Communication | Cell-cell communication analysis with SpatialCellChat |
| 05 | Visium: Differential Expression | Pseudobulk differential expression with DESeq2 and limma-voom; cell-type-specific DE with C-SIDE |
| 06 | Xenium: Analysis in R | Loading and preprocessing Xenium data, spatial clustering with MEcell, deconvolution with RCTD, and niche analysis |
These materials are provided as part of the workshop 10X Spatial Transcriptomics held on May 22nd, 2026, at the University of Chicago. The workshop covers the basics of analyzing data from 10X Genomics' Visium and Xenium platforms. Slides accompanying the tutorials can be downloaded here.
This workshop focuses on R packages. Please refer to the conda_env section for full instructions on installation of necessary tools. The tutorials page includes a summary of which packages are loaded with each tutorial section. The workshop also discusses software from 10X Genomics:
Datasets for the tutorials were obtained from 10X Genomics through their Datasets page. These include:
A scRNA dataset from Tasic et al (2016) is available as allen_cortex.rds in this Box folder.
This workshop was developed by members of the University of Chicago Center for Reseach Informatics. The associated markdown files are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.