Xenium ILC / IDC pathologist annotation breast cancer

Annotation of spatial transcriptomic breast cancer samples.

Originally created for https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03241-7

Hosted here for convenient use in the Spacehack project https://github.com/SpatialHackathon/SpaceHack2023

Data was accessed from the SubcellularSpatialData R package. Subset to unique cell ids and region annotation. Rows with missing values were removed.

Xenium data: https://www.10xgenomics.com/datasets/xenium-ffpe-human-breast-with-custom-add-on-panel-1-standard

All credit to the original authors:

Dharmesh D. Bhuva,
Chin Wee Tan,
Agus Salim,
Claire Marceaux,
Marie A. Pickering,
Jinjin Chen,
Malvika Kharbanda,
Xinyi Jin,
Ning Liu,
Kristen Feher,
Givanna Putri,
Wayne D. Tilley,
Theresa E. Hickey,
Marie-Liesse Asselin-Labat,
Belinda Phipson &
Melissa J. Davis