Companion datasets for TileScope

Repository containing data accompanying the publication "TileScope quantifies spatial gene expression relationships beyond colocalization". Analyses and results are detailed in the publication. The TileScope code is available in https://github.com/cbib/TileScope. The data are downloaded as Tilescope-data.zip, which after uncompressing has a structure is: Tilescope-data├── input_data│ ├── benchmark│ ├── file_index.csv│ ├── greenwald│ ├── mouse│ ├── overview│ ├── README.md│ └── xenium└── supplementary_data ├── README.md ├── Supplementary_Data_1.zip ├── Supplementary_Data_2.zip ├── Supplementary_Data_3.zip └── Supplementary_Data_4.zip 1. Folder input_data: Prepared spot and cell values, coordinates, ROI labels, gene definitions and run settings for the TileScope analyses. Files allow TileScope to be rerun without the original Seurat objects or raw Xenium images. Published measurements are supplied separately in bundles Supplementary Data 1–4 inside the supplementary_data folder, not repeated in this dataset. benchmark/: contains the 57 simulated datasets derived from Greenwald et al. (2024) human glioblastoma Visium data, Giraud et al. (2024) human hepatocellular carcinoma Visium data and the orthotopic mouse GL261 glioma Visium data acquired for the TileScope study (GEO data access GSE351684). It also contains files that are necessary for re-generating the corpus of simulated data. greenwald/: contains the 30 IDH-wildtype human GBM samples from Greenwald et al. (2024) mouse/: contains data from the 3 orthotopic GL261 gliomas generated for this study [Mct1_flox/flox controls (MCT1_CTL), Mct1_ΔMye myeloid (MCT1_KO) , and wild type C57BL/6N WT mouse (V4_WT) overview/: contains dat a to reproduce Fig1 from the paper README.md: description of the structure and contents of the folder xenium/: contains Xenium glioblastoma data from Meylan et al. (2026) and breast cancer data from Janesick et al. (2023) 2. Folder supplementary_data: Contains numerical results, figure data and analysis recorde for the TileScope paper. The four bundles contain the complete comparison screens as well as the selected examples shown in the figures. Tables can be read without installing TileScope REAME.md: description of the structure and contents of the folder Supplementary_Data_1.zip: bundle containing data related to the scenario benchmark Supplementary_Data_2.zip: bundle containing data related to Visium human glioblastoma Supplementary_Data_3.zip: bundle containing data related to Xenium human glioblastoma and breast cancer Supplementary_Data_4.zip: bundle containing data frelated to murine Visium glioblastoma