Pan-Cancer Single-cell Spatial Omics
About P-CaSSO
P-CaSSO is a web database for in-depth analysis of spatial transcriptomics data across multiple cancer types. Cell-type distributions in Visium slides are deconvoluted using a pan-cancer single-cell reference, enabling interactive exploration of cellular ecosystems and tumor microenvironments.
268
Visium Samples
14
Cancer Types
10+
Countries
6
Analysis Tools
Data Processing Pipeline
Integrating single-cell and spatial transcriptomics data
Data Collection
Visium slides collected from NCBI GEO, EMBL-EBI ArrayExpress, and Single Cell Portal across 14 cancer types and 10+ countries.
Processing & QC
Quality control, normalization, and batch-effect correction. Pan-cancer scRNA-seq reference with hierarchical cell-type annotation.
Deconvolution & Analysis
NNLS-based cell-type deconvolution per spot. Spatial domain analysis, co-enrichment (Jaccard index), and LR interaction scoring.
Analysis Tools
Six integrated tools for exploring the tumor spatial microenvironment
Sample Information
Browse and filter all 268 Visium samples with detailed clinical metadata
Spatial Feature Browser
Interactive H&E overlay with cell-type deconvolution and gene expression per spot
Cell-type Co-enrichment
Spatial co-localization of cell types across tumor microenvironment regions
Ligand–Receptor Analysis
Cell-cell communication networks inferred from spatially resolved LR pair expression
Proportion & Gene
Cross-sample comparison of cell-type proportions and marker gene expression
Clinical Comparison
Compare spatial transcriptomics profiles stratified by clinical variables
Data Coverage
268 Visium samples across 14 cancer types
Samples by Cancer Type
Data Types
- Visium spatial transcriptomics (10x Genomics)
- Pan-cancer scRNA-seq reference (deconvolution)
- H&E histological images (hires)
- Clinical metadata (stage, treatment, MSI, etc.)
- Spatial domain annotations (Malignant / Boundary / Normal)
Geographic Coverage
Contact & Support
P-CaSSO is a research platform for cancer spatial transcriptomics. For questions, collaboration, or technical support, please reach out.