This repository contains code to reproduce the results in Haradhvala, Yiu, Beckmann et al. Cancer Discovery 2026. Code for analyses related to the CODEX data (Figure 6-7) is availabe at zenodo along with the CODEX data.
Processed data files are available on GEO (GSE303544 [scRNA], GSE303545 [GeoMX], GSE303546 [Visium], GSE303548 [bulk RNA]). Annotated h5ad files should be downloaded and placed in the data directory to enable running scripts.