Last updated: 2025-11-19
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2025_cytoconnect_spatial_workshop/
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Cytoconnect 2025 Spatial Workshop.
For the visium analysis, we will be using the colorectal cancer data from 10x. The data can be found here.
Publication for the data:
Oliveira, M.F.d., Romero, J.P., Chung, M. et al.
High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer.
Nat Genet 57, 1512–1523 (2025).
https://doi.org/10.1038/s41588-025-02193-3| Rmd file | Topics |
|---|---|
| setup | Downloading data and packages |
Please run codes in the Rmd file before coming to the workshop.
| Rmd file | Topics |
|---|---|
| visium_01 | Introduction to data |
| Loading data into Seurat object | |
| Interacting with Seurat object | |
| visium_02 | QC and Normalisation |
| visium_03 | Visualising spatial data |
| visium_04 | Module scoring |
| Deconvolution | |
| Find Spatially Variable genes | |
| Other spatial based analyses | |