spHOT Simulation Dataset: scCube-generated spatial transcriptomics benchmarking data for spatial biomarker discovery

This dataset contains the simulation data used in the manuscript: "Phenotype-associated spatial biomarker discovery in spatial transcriptomics with spHOT" The dataset comprises five synthetic spatial transcriptomics scenarios generated using scCube (v2.0.0) from a CosMx Pouch IBD source population (GSE283625, Olivas et al. 2025). Each scenario contains 20 control and 20 case samples simulated at 2,000–4,000 cells per sample, stored as AnnData objects (.h5ad format). Scenarios included :- GT_0 : Spatial-context only, Circular spatial biomarkers only- GT_0V : Spatial-context only, Circular + Vessel-like spatial biomarkers- GT_V : Spatial-context only, Vessel-like spatial biomarkers only- GT_CC : Circular spatial biomarkers + Composition altered- GT_CCP : Circular spatial biomarkers + Composition altered + Perturbation Ground truth hotspot annotations are stored in obs['annot'], spatial coordinates in obsm['spatial'], and cell-type labels in obs['Cell_type']. Sample split information (5 fold cross-validation) are included in directory of each scenario. REPRODUCIBILITY NOTE : This dataset is generated stochastically. Accompanying code : https://github.com/DHKim327/spHOT/blob/main/tutorial/Fig2_Simulation/1.simul_scCube_V1.ipynbhttps://github.com/DHKim327/spHOT/blob/main/tutorial/Fig2_Simulation/1.simul_scCube_V2.ipynb Manuscript DOI : https://doi.org/10.64898/2026.08.11.744312 (bioRxiv)