Example Data for CellPin
This repository provides minimal example datasets for the CellPin tutorial.
The data were obtained from the 10x Genomics Xenium preview dataset:
https://www.10xgenomics.com/products/xenium-in-situ/preview-dataset-human-breast
We used In Situ Sample 1, Replicate 1 (spatial) and the corresponding FRP (scRNA-seq) sample.
The original dataset is described in:
https://www.nature.com/articles/s41467-023-43458-x
Processing summary
The scRNA-seq reference was restricted to Xenium panel genes plus 1,000 highly variable genes.
Standard quality control procedures following single cell best practices for scRNA-seq were applied.
Spatial data were subsetted, and a normalized expression layer was added.