Examples Datasets, Colab Notebooks & Reports
November 20, 2025 ยท View on GitHub
Open Problems Datasets
The following are notebooks used to run CyteType on all the single-cell datasets used for the label projection challenge in Open Problems in Single-Cell Analysis.
| Dataset | Links |
|---|---|
| Tabula Sapiens | Colab - CyteType Report - H5ad |
| GTEX v9 | Colab - CyteType Report - H5ad |
| Hypomap | Colab - CyteType Report - H5ad |
| Human Lung Cell Atlas (Core) | Colab - CyteType Report - H5ad |
| Immune Cell Atlas | Colab - CyteType Report - H5ad |
| Mouse Pancreatic Cell Atlas | Colab - CyteType Report - H5ad |
| Diabetic Kidney Disease | Colab - CyteType Report - H5ad |
CellHint Organ Atlases
CellHint auto-harmonised and auto-integrated atlas. The datasets download links are available on CellHint homepage. Data was annotated in across three notebooks: Colab 1/3, Colab 2/3, Colab 3/3
| Tissue | Links |
|---|---|
| Blood | CyteType report |
| Bone Marrow | CyteType report |
| Heart | CyteType report |
| Hippocampus | CyteType report |
| Intestine | CyteType report |
| Kidney | CyteType report |
| Liver | CyteType report |
| Lung | CyteType report |
| Lymph Node | CyteType report |
| Pancreas | CyteType report |
| Skeletal Muscle | CyteType report |
| Spleen | CyteType report |
Cell Landscapes from BIS
Cell atlases hosted by BIS from various organims and specific tissues
| Tissue | Links |
|---|---|
| Human Cell Landscape | Colab - CyteType Report - Homepage |