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README.md
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@@ -32,79 +32,79 @@ 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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| macrophage |
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| pulmonary alveolar type 2 cell |
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| capillary endothelial cell |
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| basal cell |
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| pulmonary alveolar type 1 cell |
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| intermediate monocyte |
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| CD4-positive, alpha-beta T cell |
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| CD8-positive, alpha-beta T cell |
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| endothelial cell of artery |
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| club cell |
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| classical monocyte |
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| vein endothelial cell |
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| basophil |
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| lung ciliated cell |
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| alveolar adventitial fibroblast |
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| respiratory goblet cell |
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| natural killer cell | 104 | 0.
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| pericyte |
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| B cell |
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| adventitial cell |
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| non-classical monocyte | 55 | 0.
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| monocyte |
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| neutrophil |
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| endothelial cell of lymphatic vessel |
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| bronchial smooth muscle cell |
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| mature NK T cell | 27 | 0.00 | 0.
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| plasma cell | 12 | 0.
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| vascular associated smooth muscle cell |
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63 |
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| myeloid dendritic cell | 6 | 0.00 | 0.00 | 0.
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| pulmonary ionocyte | 1 | 0.00 | 0.00 |
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| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 |
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| mesothelial cell | 1 | 0.00 | 0.50 | 0.50 | 0.50 | 0.00 | 0.
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| serous cell of epithelium of bronchus | 2 | 0.00 | 0.00 | 0.00 | 0.
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| mast cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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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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| macrophage |
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| pulmonary alveolar type 2 cell |
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| capillary endothelial cell |
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| basal cell |
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| pulmonary alveolar type 1 cell |
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79 |
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| intermediate monocyte |
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| CD4-positive, alpha-beta T cell |
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81 |
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| CD8-positive, alpha-beta T cell |
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82 |
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| endothelial cell of artery |
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83 |
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| club cell |
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84 |
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| classical monocyte |
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85 |
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| vein endothelial cell |
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86 |
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| basophil |
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| lung ciliated cell |
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88 |
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| alveolar adventitial fibroblast |
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89 |
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| respiratory goblet cell |
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90 |
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| natural killer cell | 915 | 0.
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91 |
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| pericyte |
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92 |
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| B cell |
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93 |
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| adventitial cell |
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94 |
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| non-classical monocyte | 472 | 0.26 | 0.08 | 0.
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| monocyte |
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| neutrophil |
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97 |
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| endothelial cell of lymphatic vessel |
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98 |
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| bronchial smooth muscle cell |
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99 |
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| mature NK T cell | 136 | 0.00 | 0.
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100 |
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| plasma cell | 136 | 0.
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| vascular associated smooth muscle cell |
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102 |
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| myeloid dendritic cell | 27 | 0.00 | 0.
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103 |
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| pulmonary ionocyte | 24 | 0.00 | 0.
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| plasmacytoid dendritic cell | 18 | 0.00 | 0.00 |
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| mesothelial cell | 17 | 0.00 | 0.
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| serous cell of epithelium of bronchus | 13 | 0.00 | 0.
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| mast cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.
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</details>
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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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| macrophage | 1632 | 0.96 | 0.97 | 0.98 | 0.98 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |
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| pulmonary alveolar type 2 cell | 1146 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |
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| capillary endothelial cell | 698 | 0.97 | 0.95 | 0.98 | 0.97 | 0.00 | 0.97 | 0.96 | 0.96 | 0.97 |
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| basal cell | 411 | 0.92 | 0.93 | 0.94 | 0.93 | 0.00 | 0.94 | 0.93 | 0.93 | 0.95 |
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| pulmonary alveolar type 1 cell | 302 | 0.98 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
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| intermediate monocyte | 278 | 0.64 | 0.62 | 0.67 | 0.69 | 0.00 | 0.54 | 0.77 | 0.84 | 0.77 |
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| CD4-positive, alpha-beta T cell | 206 | 0.87 | 0.89 | 0.85 | 0.85 | 0.00 | 0.89 | 0.88 | 0.90 | 0.91 |
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| CD8-positive, alpha-beta T cell | 201 | 0.85 | 0.86 | 0.78 | 0.80 | 0.00 | 0.88 | 0.83 | 0.87 | 0.87 |
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| endothelial cell of artery | 158 | 0.79 | 0.78 | 0.84 | 0.75 | 0.00 | 0.81 | 0.77 | 0.79 | 0.82 |
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| club cell | 181 | 0.82 | 0.82 | 0.85 | 0.83 | 0.00 | 0.83 | 0.85 | 0.83 | 0.87 |
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| classical monocyte | 154 | 0.58 | 0.57 | 0.61 | 0.61 | 0.00 | 0.57 | 0.73 | 0.89 | 0.74 |
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| vein endothelial cell | 142 | 0.81 | 0.80 | 0.87 | 0.79 | 0.00 | 0.84 | 0.81 | 0.84 | 0.85 |
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| basophil | 145 | 0.97 | 0.99 | 0.99 | 1.00 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |
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| lung ciliated cell | 134 | 0.97 | 0.99 | 0.99 | 0.99 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |
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| alveolar adventitial fibroblast | 117 | 0.85 | 0.86 | 0.86 | 0.90 | 0.00 | 0.90 | 0.91 | 0.91 | 0.94 |
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| respiratory goblet cell | 107 | 0.76 | 0.82 | 0.83 | 0.80 | 0.00 | 0.84 | 0.83 | 0.83 | 0.84 |
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| natural killer cell | 104 | 0.87 | 0.88 | 0.87 | 0.85 | 0.00 | 0.90 | 0.87 | 0.89 | 0.90 |
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| pericyte | 76 | 0.79 | 0.86 | 0.88 | 0.89 | 0.00 | 0.90 | 0.90 | 0.92 | 0.92 |
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| B cell | 67 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
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| adventitial cell | 61 | 0.68 | 0.83 | 0.81 | 0.85 | 0.00 | 0.85 | 0.87 | 0.88 | 0.90 |
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| non-classical monocyte | 55 | 0.32 | 0.11 | 0.34 | 0.06 | 0.00 | 0.36 | 0.56 | 0.77 | 0.55 |
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| monocyte | 51 | 0.42 | 0.33 | 0.38 | 0.46 | 0.00 | 0.32 | 0.48 | 0.72 | 0.58 |
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| neutrophil | 35 | 0.92 | 0.97 | 0.94 | 0.94 | 0.00 | 0.96 | 0.97 | 0.89 | 0.96 |
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| endothelial cell of lymphatic vessel | 32 | 0.96 | 0.97 | 0.92 | 0.96 | 0.00 | 0.94 | 0.97 | 0.97 | 0.98 |
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| bronchial smooth muscle cell | 24 | 0.49 | 0.48 | 0.69 | 0.51 | 0.00 | 0.54 | 0.64 | 0.78 | 0.73 |
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| mature NK T cell | 27 | 0.00 | 0.25 | 0.31 | 0.21 | 0.00 | 0.56 | 0.48 | 0.51 | 0.45 |
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| plasma cell | 12 | 0.87 | 0.85 | 0.92 | 0.96 | 0.00 | 0.92 | 0.89 | 0.92 | 0.96 |
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| vascular associated smooth muscle cell | 18 | 0.53 | 0.52 | 0.47 | 0.64 | 0.00 | 0.79 | 0.76 | 0.75 | 0.73 |
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| myeloid dendritic cell | 6 | 0.00 | 0.00 | 0.83 | 0.80 | 0.00 | 0.77 | 0.67 | 0.92 | 0.91 |
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| pulmonary ionocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 0.00 |
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| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 1.00 | 0.67 | 0.00 | 0.40 | 1.00 | 1.00 | 1.00 |
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| mesothelial cell | 1 | 0.00 | 0.50 | 0.50 | 0.50 | 0.00 | 0.40 | 0.40 | 0.50 | 0.50 |
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| serous cell of epithelium of bronchus | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.40 | 0.80 | 1.00 | 0.00 |
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| mast cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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The train accuracies are computed on the training data.
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71 |
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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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| macrophage | 14854 | 0.96 | 0.98 | 0.98 | 0.98 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |
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| pulmonary alveolar type 2 cell | 10448 | 0.97 | 0.97 | 0.99 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |
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| capillary endothelial cell | 6545 | 0.97 | 0.96 | 0.98 | 0.98 | 0.00 | 0.97 | 0.96 | 0.96 | 0.98 |
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| basal cell | 3604 | 0.92 | 0.94 | 0.96 | 0.96 | 0.00 | 0.94 | 0.95 | 0.95 | 0.97 |
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| pulmonary alveolar type 1 cell | 2814 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.97 | 0.98 |
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| intermediate monocyte | 2507 | 0.62 | 0.62 | 0.78 | 0.78 | 0.00 | 0.63 | 0.81 | 0.87 | 0.83 |
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| CD4-positive, alpha-beta T cell | 1918 | 0.87 | 0.87 | 0.90 | 0.90 | 0.00 | 0.91 | 0.90 | 0.92 | 0.93 |
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| CD8-positive, alpha-beta T cell | 1697 | 0.85 | 0.83 | 0.87 | 0.87 | 0.00 | 0.89 | 0.87 | 0.90 | 0.91 |
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| endothelial cell of artery | 1596 | 0.78 | 0.79 | 0.86 | 0.85 | 0.00 | 0.82 | 0.82 | 0.83 | 0.86 |
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| club cell | 1566 | 0.82 | 0.82 | 0.91 | 0.90 | 0.00 | 0.86 | 0.88 | 0.86 | 0.91 |
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84 |
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| classical monocyte | 1415 | 0.60 | 0.56 | 0.72 | 0.71 | 0.00 | 0.71 | 0.81 | 0.93 | 0.84 |
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| vein endothelial cell | 1194 | 0.81 | 0.81 | 0.88 | 0.86 | 0.00 | 0.85 | 0.86 | 0.89 | 0.88 |
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86 |
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| basophil | 1177 | 0.97 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |
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87 |
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| lung ciliated cell | 1075 | 0.96 | 0.97 | 0.99 | 0.99 | 0.00 | 0.95 | 0.98 | 0.98 | 0.98 |
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88 |
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| alveolar adventitial fibroblast | 996 | 0.87 | 0.85 | 0.89 | 0.94 | 0.00 | 0.93 | 0.96 | 0.97 | 0.96 |
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89 |
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| respiratory goblet cell | 933 | 0.80 | 0.86 | 0.89 | 0.89 | 0.00 | 0.87 | 0.88 | 0.88 | 0.91 |
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| natural killer cell | 915 | 0.90 | 0.91 | 0.93 | 0.93 | 0.00 | 0.94 | 0.95 | 0.96 | 0.96 |
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91 |
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| pericyte | 663 | 0.78 | 0.89 | 0.94 | 0.92 | 0.00 | 0.95 | 0.98 | 0.98 | 0.97 |
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| B cell | 596 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
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| adventitial cell | 520 | 0.75 | 0.80 | 0.83 | 0.91 | 0.00 | 0.91 | 0.95 | 0.96 | 0.95 |
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| non-classical monocyte | 472 | 0.26 | 0.08 | 0.34 | 0.30 | 0.00 | 0.45 | 0.71 | 0.80 | 0.68 |
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| monocyte | 455 | 0.43 | 0.27 | 0.53 | 0.53 | 0.00 | 0.49 | 0.76 | 0.83 | 0.77 |
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| neutrophil | 336 | 0.93 | 0.97 | 0.98 | 0.96 | 0.00 | 0.97 | 0.99 | 0.95 | 0.99 |
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| endothelial cell of lymphatic vessel | 283 | 0.96 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.99 | 0.98 |
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| bronchial smooth muscle cell | 196 | 0.50 | 0.55 | 0.77 | 0.60 | 0.00 | 0.80 | 0.91 | 0.95 | 0.91 |
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| mature NK T cell | 136 | 0.00 | 0.15 | 0.53 | 0.40 | 0.00 | 0.70 | 0.83 | 0.91 | 0.91 |
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| plasma cell | 136 | 0.81 | 0.83 | 0.95 | 0.94 | 0.00 | 0.94 | 0.97 | 0.94 | 0.98 |
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101 |
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| vascular associated smooth muscle cell | 113 | 0.48 | 0.50 | 0.75 | 0.61 | 0.00 | 0.83 | 0.95 | 0.95 | 0.94 |
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102 |
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| myeloid dendritic cell | 27 | 0.00 | 0.12 | 0.84 | 0.73 | 0.00 | 0.77 | 0.93 | 0.90 | 0.96 |
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103 |
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| pulmonary ionocyte | 24 | 0.00 | 0.89 | 0.98 | 0.88 | 0.00 | 0.79 | 0.96 | 0.94 | 0.96 |
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104 |
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| plasmacytoid dendritic cell | 18 | 0.00 | 0.00 | 0.95 | 0.95 | 0.00 | 0.86 | 0.97 | 0.97 | 0.97 |
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105 |
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| mesothelial cell | 17 | 0.00 | 0.79 | 0.81 | 0.77 | 0.00 | 0.60 | 0.92 | 0.87 | 0.83 |
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106 |
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| serous cell of epithelium of bronchus | 13 | 0.00 | 0.00 | 0.64 | 0.27 | 0.00 | 0.68 | 0.90 | 0.93 | 0.70 |
|
107 |
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| mast cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 1.00 | 0.86 | 0.50 |
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</details>
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