Authors: Jason Shapiro, Ph.D. and Diana Vera Cruz, Ph.D.
| Topic | Materials | Type |
|---|---|---|
| Overview | Slides | Slides |
| Visium Example 1 | Seurat vignette | Markdown and Rmd |
| Visium Example 2 | Tumor microenvironment | Markdown and Rmd |
| GeoMx QC | 1_geomx_setup_qc | Markdown and Rmd |
| GeoMx DE Geomxtools | 2_geomx_norm_DE | Markdown and Rmd |
| GeoMx DE standR,limma | 2B_geomx_standR_norm_DE | Markdown and Rmd |
| GeoMx DE limma | 2C_geomx_limma_norm_DE | Markdown and Rmd |
| GeoMx - Spatial Deconvolution | geomx_SpatialDecon | Markdown and Rmd |
| GeoMx - Seurat conversion | geomx_Seurat | Markdown and Rmd |
These materials are provided as part of the workshop Introduction to Spatial Transcriptomics held on April 3rd, 2025, at the University of Chicago. The workshop covers the basics of analyzing data from 10X Genomics' Visium platform and NanoString's GeoMx platform. For additional details on the example code and datasets used for each section, please start from the separate folders for Visium or GeoMx.
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.