Demonstration datasets for Spatial Omics Toolkit 2 (sotk2)

This Zenodo record provides demonstration data for the Spatial Omics Toolkit 2 (sotk2). The collection includes three publicly available transcriptomics datasets spanning bulk RNA-seq and spatial transcriptomics modalities: GLASS (Glioma Longitudinal AnalySiS Consortium): bulk RNA-seq from matched primary and recurrent glioma samples IVYGAP (Ivy Glioblastoma Atlas Project): bulk RNA-seq stratified by anatomic features (CT, IT, LE, MVP, PAN) HEILAND (Ravi et al., Cancer Cell, 2022): 10x Genomics Visium v1 spatial transcriptomics For reproducible downstream use and improved demonstration workflows, the original data were imported into R and re-exported as binary R objects (.rds). Each dataset contains the following components: GLASS: cNMF results, bulk RNA-seq expression data, and sample annotations IVYGAP: cNMF results HEILAND: cNMF results, a Seurat object for the Visium data and a spot coordinate file for one sample (UKF269_T) Primary sources used for acquisition: GLASS: https://www.synapse.org/glass (PMID: 29432615) IVYGAP: https://glioblastoma.alleninstitute.org/ (PMID: 29748285) HEILAND: https://doi.org/10.5061/dryad.h70rxwdmj (PMID: 35700707) For documentation, usage examples, and sotk2 workflows, see: https://www.github.com/Snyder-Institute/sotk2 Note: Among the files, soObj.RDS was preprocessed using the sotk2 package, allowing users to bypass pre-calculation and use it directly for visualization and interpretation.