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README.md
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@@ -5,7 +5,8 @@ tags:
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- biology
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- genomics
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- single-cell
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- anndata_version:0.11.
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- popV
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- 'tissue: Thymus'
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---
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@@ -31,35 +32,35 @@ computed on a 10% random subset of the data that was not used for training.
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| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
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| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
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| CD4-positive, alpha-beta T cell | 745 | 0.
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| CD4-positive, alpha-beta thymocyte |
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| B cell |
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| thymic fibroblast type 2 |
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| thymic fibroblast type 1 |
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| CD8-positive, alpha-beta T cell |
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| capillary endothelial cell |
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| naive thymus-derived CD4-positive, alpha-beta T cell |
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| smooth muscle cell |
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| vein endothelial cell | 213 | 0.
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| plasma cell |
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| endothelial cell of artery |
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| macrophage |
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| CD8-positive, alpha-beta thymocyte |
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| thymocyte |
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| naive thymus-derived CD8-positive, alpha-beta T cell |
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| natural killer cell |
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| endothelial cell of lymphatic vessel | 35 | 1.00 | 1.00 | 1.00 | 0.
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| fibroblast | 22 | 0.
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| vascular associated smooth muscle cell |
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| mesothelial cell |
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| erythrocyte |
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| neuro-medullary thymic epithelial cell |
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| neutrophil |
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| hematopoietic precursor cell | 10 | 0.80 | 0.
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| myo-medullary thymic epithelial cell | 5 | 0.
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| medullary thymic epithelial cell | 7 | 1.00 | 0.
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| monocyte |
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| mast cell |
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| fast muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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| T follicular helper cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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| innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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@@ -69,39 +70,39 @@ The train accuracies are computed on the training data.
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| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
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| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
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| CD4-positive, alpha-beta T cell | 6381 | 0.
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| CD4-positive, alpha-beta thymocyte |
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| B cell |
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| thymic fibroblast type 2 |
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| thymic fibroblast type 1 |
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| CD8-positive, alpha-beta T cell |
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| capillary endothelial cell |
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| naive thymus-derived CD4-positive, alpha-beta T cell |
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| smooth muscle cell |
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| vein endothelial cell | 1835 | 0.
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| plasma cell |
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| endothelial cell of artery |
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| macrophage |
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| CD8-positive, alpha-beta thymocyte |
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| thymocyte |
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| naive thymus-derived CD8-positive, alpha-beta T cell |
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| natural killer cell |
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| endothelial cell of lymphatic vessel | 336 | 0.97 | 0.97 | 0.98 | 0.
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| fibroblast | 250 | 0.
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| vascular associated smooth muscle cell |
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| mesothelial cell |
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| erythrocyte |
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| neuro-medullary thymic epithelial cell |
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| neutrophil |
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| hematopoietic precursor cell | 82 | 0.74 | 0.
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| myo-medullary thymic epithelial cell | 72 | 0.
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| medullary thymic epithelial cell | 36 | 0.
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| monocyte |
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| mast cell |
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| fast muscle cell | 21 | 0.
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| T follicular helper cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.
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| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.
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| endothelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.
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</details>
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- biology
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- genomics
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- single-cell
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- anndata_version:0.11.3
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- python_version:3.11.11
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- popV
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- 'tissue: Thymus'
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---
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| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
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| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
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| CD4-positive, alpha-beta T cell | 745 | 0.77 | 0.85 | 0.84 | 0.79 | 0.00 | 0.73 | 0.73 | 0.78 | 0.85 |
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| CD4-positive, alpha-beta thymocyte | 424 | 0.66 | 0.53 | 0.74 | 0.67 | 0.00 | 0.63 | 0.63 | 0.71 | 0.73 |
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| B cell | 453 | 1.00 | 0.99 | 0.99 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
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| thymic fibroblast type 2 | 381 | 0.87 | 0.90 | 0.89 | 0.90 | 0.00 | 0.92 | 0.89 | 0.91 | 0.94 |
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| thymic fibroblast type 1 | 337 | 0.88 | 0.87 | 0.89 | 0.88 | 0.00 | 0.92 | 0.89 | 0.90 | 0.93 |
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| CD8-positive, alpha-beta T cell | 290 | 0.81 | 0.86 | 0.86 | 0.81 | 0.00 | 0.86 | 0.84 | 0.86 | 0.87 |
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| capillary endothelial cell | 275 | 0.83 | 0.86 | 0.90 | 0.83 | 0.00 | 0.83 | 0.84 | 0.84 | 0.88 |
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| naive thymus-derived CD4-positive, alpha-beta T cell | 261 | 0.49 | 0.46 | 0.49 | 0.39 | 0.00 | 0.53 | 0.40 | 0.52 | 0.57 |
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| smooth muscle cell | 223 | 0.98 | 0.96 | 0.97 | 0.97 | 0.00 | 0.98 | 0.99 | 0.98 | 0.98 |
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| vein endothelial cell | 213 | 0.84 | 0.84 | 0.89 | 0.82 | 0.00 | 0.84 | 0.85 | 0.85 | 0.88 |
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| plasma cell | 138 | 1.00 | 0.99 | 0.99 | 0.99 | 0.00 | 1.00 | 1.00 | 1.00 | 0.99 |
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| endothelial cell of artery | 85 | 0.84 | 0.93 | 0.92 | 0.80 | 0.00 | 0.88 | 0.91 | 0.91 | 0.94 |
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| macrophage | 87 | 0.97 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |
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| CD8-positive, alpha-beta thymocyte | 74 | 0.62 | 0.71 | 0.79 | 0.46 | 0.00 | 0.76 | 0.62 | 0.74 | 0.80 |
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| thymocyte | 48 | 0.52 | 0.60 | 0.78 | 0.41 | 0.00 | 0.76 | 0.61 | 0.75 | 0.81 |
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| naive thymus-derived CD8-positive, alpha-beta T cell | 38 | 0.30 | 0.47 | 0.49 | 0.13 | 0.00 | 0.38 | 0.50 | 0.56 | 0.58 |
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| natural killer cell | 44 | 0.97 | 0.98 | 0.97 | 0.89 | 0.00 | 0.97 | 0.96 | 0.93 | 0.97 |
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| endothelial cell of lymphatic vessel | 35 | 1.00 | 1.00 | 1.00 | 0.94 | 0.00 | 0.96 | 0.99 | 0.99 | 1.00 |
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| fibroblast | 22 | 0.53 | 0.16 | 0.21 | 0.65 | 0.00 | 0.88 | 0.75 | 0.86 | 0.93 |
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| vascular associated smooth muscle cell | 15 | 0.74 | 0.00 | 0.57 | 0.58 | 0.00 | 0.82 | 0.97 | 0.87 | 0.77 |
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| mesothelial cell | 15 | 0.93 | 0.89 | 0.97 | 0.90 | 0.00 | 0.87 | 0.93 | 0.90 | 0.97 |
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| erythrocyte | 17 | 0.91 | 0.94 | 0.91 | 0.97 | 0.00 | 0.94 | 0.97 | 0.97 | 0.94 |
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| neuro-medullary thymic epithelial cell | 15 | 0.97 | 0.97 | 0.93 | 0.90 | 0.00 | 0.87 | 1.00 | 0.97 | 1.00 |
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| neutrophil | 12 | 0.74 | 0.92 | 0.92 | 0.83 | 0.00 | 0.88 | 0.92 | 0.87 | 0.88 |
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| hematopoietic precursor cell | 10 | 0.80 | 0.46 | 0.95 | 0.80 | 0.00 | 0.70 | 0.89 | 0.86 | 0.84 |
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| myo-medullary thymic epithelial cell | 5 | 0.91 | 0.75 | 1.00 | 0.80 | 0.00 | 0.91 | 0.91 | 1.00 | 0.91 |
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| medullary thymic epithelial cell | 7 | 1.00 | 0.67 | 0.55 | 0.67 | 0.00 | 0.92 | 0.92 | 1.00 | 0.92 |
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| monocyte | 1 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 0.00 |
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| mast cell | 3 | 0.00 | 0.80 | 0.80 | 0.80 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |
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| fast muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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| T follicular helper cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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| innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
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| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
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| CD4-positive, alpha-beta T cell | 6381 | 0.76 | 0.81 | 0.89 | 0.81 | 0.00 | 0.73 | 0.75 | 0.78 | 0.86 |
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| CD4-positive, alpha-beta thymocyte | 4139 | 0.69 | 0.45 | 0.84 | 0.77 | 0.00 | 0.73 | 0.70 | 0.75 | 0.81 |
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| B cell | 4009 | 1.00 | 0.99 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
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| thymic fibroblast type 2 | 3824 | 0.88 | 0.90 | 0.94 | 0.93 | 0.00 | 0.93 | 0.92 | 0.92 | 0.94 |
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| thymic fibroblast type 1 | 2933 | 0.86 | 0.86 | 0.93 | 0.91 | 0.00 | 0.91 | 0.90 | 0.90 | 0.93 |
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| CD8-positive, alpha-beta T cell | 2527 | 0.79 | 0.83 | 0.90 | 0.85 | 0.00 | 0.83 | 0.82 | 0.84 | 0.87 |
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| capillary endothelial cell | 2346 | 0.82 | 0.85 | 0.94 | 0.89 | 0.00 | 0.89 | 0.89 | 0.88 | 0.92 |
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| naive thymus-derived CD4-positive, alpha-beta T cell | 2262 | 0.49 | 0.41 | 0.66 | 0.55 | 0.00 | 0.57 | 0.51 | 0.58 | 0.65 |
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| smooth muscle cell | 2002 | 0.96 | 0.94 | 0.99 | 0.98 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |
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| vein endothelial cell | 1835 | 0.82 | 0.82 | 0.93 | 0.88 | 0.00 | 0.88 | 0.89 | 0.88 | 0.91 |
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| plasma cell | 1440 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
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| endothelial cell of artery | 688 | 0.89 | 0.92 | 0.96 | 0.88 | 0.00 | 0.93 | 0.96 | 0.94 | 0.97 |
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| macrophage | 683 | 0.97 | 0.98 | 0.99 | 0.97 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
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| CD8-positive, alpha-beta thymocyte | 598 | 0.59 | 0.69 | 0.84 | 0.64 | 0.00 | 0.77 | 0.75 | 0.81 | 0.84 |
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| thymocyte | 407 | 0.57 | 0.62 | 0.83 | 0.47 | 0.00 | 0.86 | 0.79 | 0.87 | 0.91 |
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| naive thymus-derived CD8-positive, alpha-beta T cell | 396 | 0.36 | 0.43 | 0.71 | 0.21 | 0.00 | 0.57 | 0.67 | 0.75 | 0.78 |
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| natural killer cell | 384 | 0.91 | 0.91 | 0.94 | 0.86 | 0.00 | 0.94 | 0.97 | 0.96 | 0.97 |
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| endothelial cell of lymphatic vessel | 336 | 0.97 | 0.97 | 0.98 | 0.93 | 0.00 | 0.94 | 0.99 | 0.98 | 0.99 |
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| fibroblast | 250 | 0.66 | 0.06 | 0.95 | 0.85 | 0.00 | 0.97 | 0.89 | 0.93 | 0.97 |
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| vascular associated smooth muscle cell | 226 | 0.69 | 0.04 | 0.96 | 0.84 | 0.00 | 0.93 | 0.97 | 0.95 | 0.98 |
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| mesothelial cell | 160 | 0.94 | 0.84 | 0.95 | 0.93 | 0.00 | 0.97 | 0.98 | 0.98 | 0.97 |
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| erythrocyte | 135 | 0.95 | 0.92 | 0.92 | 0.96 | 0.00 | 0.93 | 0.99 | 0.94 | 0.97 |
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| neuro-medullary thymic epithelial cell | 120 | 0.92 | 0.92 | 0.90 | 0.91 | 0.00 | 0.90 | 1.00 | 0.99 | 0.98 |
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| neutrophil | 109 | 0.61 | 0.78 | 0.90 | 0.86 | 0.00 | 0.96 | 1.00 | 1.00 | 1.00 |
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| hematopoietic precursor cell | 82 | 0.74 | 0.11 | 0.88 | 0.91 | 0.00 | 0.98 | 1.00 | 0.98 | 1.00 |
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| myo-medullary thymic epithelial cell | 72 | 0.81 | 0.85 | 0.96 | 0.94 | 0.00 | 0.98 | 0.99 | 1.00 | 0.98 |
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| medullary thymic epithelial cell | 36 | 0.86 | 0.52 | 0.87 | 0.76 | 0.00 | 0.99 | 1.00 | 1.00 | 0.96 |
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| monocyte | 25 | 0.00 | 0.00 | 0.82 | 0.62 | 0.00 | 0.86 | 0.98 | 0.96 | 1.00 |
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| mast cell | 21 | 0.00 | 0.84 | 0.89 | 0.85 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
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| fast muscle cell | 21 | 0.54 | 0.15 | 0.95 | 0.86 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |
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| T follicular helper cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.43 | 0.86 | 0.86 | 0.91 |
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| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.57 | 1.00 | 1.00 |
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| endothelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.22 | 1.00 | 1.00 | 1.00 |
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</details>
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