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Author: suu-yi

docs/examples.md

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+# Examples Datasets, Colab Notebooks & Reports
+
+## 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](https://openproblems.bio/benchmarks/label_projection/). 
+
+| Dataset | Links |
+| --- | --- |
+| **Tabula Sapiens** | [Colab](https://colab.research.google.com/drive/1EyQXaruDJBPICUvlUY1E19zxOm_L4_VU?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/15332f10-2048-4099-ab1e-baf2ab9e39c3) - [H5ad](https://drive.google.com/file/d/1URo7niPqAo-9HGVH8f3QJfqll9lc8JN_/view?usp=drive_link) |
+| **GTEX v9** | [Colab](https://colab.research.google.com/drive/1uvqG2eVaUuNe66e0_7bp682uCdKx6-KL?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/5242f3b8-0078-417d-954e-00d1bb19bdf6) - [H5ad](https://drive.google.com/file/d/1EIpudRyasLUHR6J2v8fdpmBTbCE2__UF/view?usp=drive_link) |
+| **Hypomap** | [Colab](https://colab.research.google.com/drive/1OuTnh8xHoXaINCGcgu_1q-jANwXL8ggF?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/3840b662-bacf-4067-b93d-4e57c1f21187) - [H5ad](https://drive.google.com/file/d/1QMvZNdoDlKpOmyguAXSk45-YVz97v4tM/view?usp=drive_link) |
+| **Human Lung Cell Atlas (Core)** | [Colab](https://colab.research.google.com/drive/1FoTD-XzLNDPgYSlgVsxnLwPnWF5YiKny?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/6da1458a-392f-4bce-b6c9-4ccb308c8797) - [H5ad](https://drive.google.com/file/d/13O0dyUnwJKLPm8fncRt597S5hs2COsxx/view?usp=drive_link) |
+| **Immune Cell Atlas** | [Colab](https://colab.research.google.com/drive/1Kum9S_kU76QvS__42ABd-Xp1GpH4c9jU?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/05ff7629-8f0c-4b95-ac65-30bba9b384c5) - [H5ad](https://drive.google.com/file/d/1iqkC7dG1ovgKsU_8HdZ2eyELIxB0sM3t/view?usp=drive_link) |
+| **Mouse Pancreatic Cell Atlas** | [Colab](https://colab.research.google.com/drive/1fg9W3Lz-E_yAVoqs_6XrQsYkfsfnzFey?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/6d248cd2-6b61-4beb-bc58-1d63c7a2fc34) - [H5ad](https://drive.google.com/file/d/19qpRfz4WGuUsRNl0YKuy3YENfHKI6pz-/view?usp=drive_link) |
+| **Diabetic Kidney Disease** | [Colab](https://colab.research.google.com/drive/1kb3urFbl0PEPW4T_ti0DBTAmi5YK_-t1?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/0da4eaef-f165-4800-a4e3-c5cf8ec165ad) - [H5ad](https://drive.google.com/file/d/1yZXYlfZHLYcPL18Jy25J4v8kWQYhSsd7/view?usp=drive_link) |
+
+## CellHint Organ Atlases
+
+CellHint auto-harmonised and auto-integrated atlas. The datasets download links are available on CellHint [homepage](https://www.celltypist.org/organs).
+Data was annotated in across three notebooks: [Colab 1/3](https://colab.research.google.com/drive/1-O4UJ9m1hP36DoO8zMz5PtwXCSc66gpX?usp=sharing), [Colab 2/3](https://colab.research.google.com/drive/1QvcqVr_RPvEWntY0dpidJVz6OMhP2L6M?usp=sharing), [Colab 3/3](https://colab.research.google.com/drive/1Srd2GhvJqL7LIt21OsJLtN-z8QRshIqt?usp=sharing)
+
+| Tissue | Links |
+| --- | --- |
+| **Blood** | [CyteType report](https://prod.cytetype.nygen.io/report/d0c219b4-2b4a-4b27-bac9-aea280a972f1) |
+| **Bone Marrow** | [CyteType report](https://prod.cytetype.nygen.io/report/bc5099b5-42c2-4ba7-8fdd-bc7b5dd3e84d) |
+| **Heart** | [CyteType report](https://prod.cytetype.nygen.io/report/2ffd6cf1-ec98-43d1-82d7-1fc3e9a11b8c) |
+| **Hippocampus** | [CyteType report](https://prod.cytetype.nygen.io/report/60b98429-2338-4408-a07c-bb60e82ac793) |
+| **Intestine** | [CyteType report](https://prod.cytetype.nygen.io/report/e0a2ca37-872f-489c-8de1-d84434d409fe) |
+| **Kidney** | [CyteType report](https://prod.cytetype.nygen.io/report/7dd1f0ea-7eec-4968-b353-8b52707de5ac) |
+| **Liver** | [CyteType report](https://prod.cytetype.nygen.io/report/a429348c-530a-486c-8980-3349a583b8c4) |
+| **Lung** | [CyteType report](https://prod.cytetype.nygen.io/report/75e41a21-f771-4ebc-829a-82f93529a147) |
+| **Lymph Node** | [CyteType report](https://prod.cytetype.nygen.io/report/b911e212-fe37-4bdc-a7f3-51e9146bf8cc) |
+| **Pancreas** | [CyteType report](https://prod.cytetype.nygen.io/report/b620245a-1ae0-4025-aab7-52ada6dcc6cb) |
+| **Skeletal Muscle** | [CyteType report](https://prod.cytetype.nygen.io/report/3f35a45d-aa1b-42cb-92d2-e739623a402b) |
+| **Spleen** | [CyteType report](https://prod.cytetype.nygen.io/report/4b64ec02-ac01-45b5-84b9-0f16708cbd85) |
+
+## Cell Landscapes from BIS
+Cell atlases hosted by [BIS](https://bis.zju.edu.cn/) from various organims and specific tissues
+
+| Tissue | Links |
+| --- | --- |
+| Human Cell Landscape | [Colab](https://colab.research.google.com/drive/1czLW33FYbnPOmPvnfddsvehXM491UDGq?usp=sharing) - [CyteType Report](https://prod.cytetype.nygen.io/report/581616bf-3c96-4e58-a290-881b40378309) - [Homepage](https://bis.zju.edu.cn/HCL/) |