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OnClass.data-00000-of-00001

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OnClass.npz

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accuracies.json

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 {
-    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| classical monocyte | 780 | 0.94 | 0.92 | 0.94 | 0.95 | 0.00 | 0.91 | 0.91 | 0.91 | 0.95 |\n| bronchial smooth muscle cell | 228 | 0.98 | 0.98 | 0.98 | 0.96 | 0.00 | 0.98 | 0.98 | 0.97 | 0.99 |\n| intermediate monocyte | 174 | 0.76 | 0.54 | 0.72 | 0.78 | 0.00 | 0.73 | 0.66 | 0.69 | 0.79 |\n| fibroblast of lung | 139 | 0.98 | 0.97 | 0.97 | 0.92 | 0.00 | 0.98 | 0.98 | 0.97 | 0.98 |\n| B cell | 151 | 1.00 | 1.00 | 0.98 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| alveolar macrophage | 142 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.98 | 0.98 | 0.99 |\n| natural killer cell | 125 | 0.99 | 0.99 | 0.97 | 0.96 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |\n| lung macrophage | 122 | 0.97 | 0.92 | 0.96 | 0.95 | 0.00 | 0.96 | 0.95 | 0.95 | 0.96 |\n| non-classical monocyte | 94 | 0.96 | 0.83 | 0.89 | 0.94 | 0.00 | 0.95 | 0.95 | 0.93 | 0.97 |\n| CD8-positive, alpha-beta T cell | 85 | 0.88 | 0.88 | 0.85 | 0.78 | 0.00 | 0.88 | 0.87 | 0.89 | 0.90 |\n| neutrophil | 70 | 1.00 | 0.97 | 0.97 | 0.99 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |\n| CD4-positive, alpha-beta T cell | 54 | 0.77 | 0.80 | 0.80 | 0.71 | 0.00 | 0.88 | 0.82 | 0.85 | 0.84 |\n| adventitial cell | 60 | 0.95 | 0.95 | 0.93 | 0.83 | 0.00 | 0.94 | 0.96 | 0.92 | 0.94 |\n| mature NK T cell | 43 | 0.92 | 0.91 | 0.93 | 0.75 | 0.00 | 0.92 | 0.94 | 0.90 | 0.94 |\n| vein endothelial cell | 33 | 0.93 | 0.94 | 0.87 | 0.68 | 0.00 | 0.93 | 0.96 | 0.85 | 0.97 |\n| T cell | 28 | 0.94 | 0.96 | 0.96 | 0.89 | 0.00 | 0.93 | 0.95 | 0.93 | 0.98 |\n| myeloid dendritic cell | 22 | 0.88 | 0.90 | 0.88 | 0.89 | 0.00 | 0.62 | 0.84 | 0.79 | 0.89 |\n| pulmonary interstitial fibroblast | 21 | 1.00 | 1.00 | 0.98 | 0.98 | 0.00 | 0.98 | 1.00 | 0.98 | 0.98 |\n| basophil | 9 | 0.95 | 0.80 | 0.89 | 0.67 | 0.00 | 0.67 | 0.70 | 0.74 | 0.89 |\n| regulatory T cell | 12 | 0.00 | 0.67 | 0.59 | 0.76 | 0.00 | 0.88 | 0.88 | 0.86 | 0.74 |\n| smooth muscle cell of the pulmonary artery | 14 | 0.83 | 0.88 | 0.92 | 0.53 | 0.00 | 0.89 | 0.86 | 0.86 | 0.92 |\n| plasmacytoid dendritic cell | 8 | 0.93 | 0.93 | 0.93 | 0.93 | 0.00 | 0.84 | 0.93 | 0.93 | 1.00 |\n| pericyte | 6 | 1.00 | 1.00 | 1.00 | 0.92 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| ciliated columnar cell of tracheobronchial tree | 10 | 0.91 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| plasma cell | 1 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 0.67 | 1.00 | 1.00 |\n| dendritic cell | 3 | 0.00 | 0.50 | 0.40 | 0.40 | 0.00 | 0.31 | 0.50 | 0.57 | 0.40 |\n| endothelial cell of lymphatic vessel | 4 | 1.00 | 1.00 | 0.86 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| club cell | 4 | 0.22 | 0.00 | 0.40 | 0.40 | 0.00 | 0.40 | 0.47 | 0.40 | 0.40 |\n| lung neuroendocrine cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
-    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| classical monocyte | 7142 | 0.93 | 0.92 | 0.96 | 0.97 | 0.00 | 0.90 | 0.92 | 0.92 | 0.97 |\n| bronchial smooth muscle cell | 2111 | 0.98 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| intermediate monocyte | 1575 | 0.73 | 0.51 | 0.79 | 0.84 | 0.00 | 0.74 | 0.72 | 0.74 | 0.87 |\n| fibroblast of lung | 1384 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| B cell | 1350 | 1.00 | 1.00 | 0.99 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| alveolar macrophage | 1224 | 0.99 | 0.97 | 0.98 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| natural killer cell | 1068 | 0.99 | 0.99 | 0.96 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| lung macrophage | 1035 | 0.96 | 0.93 | 0.97 | 0.96 | 0.00 | 0.95 | 0.96 | 0.95 | 0.98 |\n| non-classical monocyte | 916 | 0.97 | 0.84 | 0.92 | 0.97 | 0.00 | 0.96 | 0.97 | 0.97 | 0.98 |\n| CD8-positive, alpha-beta T cell | 785 | 0.89 | 0.90 | 0.88 | 0.86 | 0.00 | 0.92 | 0.97 | 0.98 | 0.94 |\n| neutrophil | 482 | 1.00 | 0.97 | 0.98 | 0.99 | 0.00 | 0.95 | 1.00 | 0.98 | 1.00 |\n| CD4-positive, alpha-beta T cell | 497 | 0.76 | 0.80 | 0.85 | 0.77 | 0.00 | 0.90 | 0.97 | 0.98 | 0.91 |\n| adventitial cell | 466 | 0.92 | 0.94 | 0.95 | 0.94 | 0.00 | 0.96 | 0.98 | 0.97 | 0.97 |\n| mature NK T cell | 377 | 0.84 | 0.86 | 0.86 | 0.85 | 0.00 | 0.93 | 0.98 | 0.98 | 0.94 |\n| vein endothelial cell | 287 | 0.93 | 0.96 | 0.95 | 0.80 | 0.00 | 0.92 | 0.95 | 0.94 | 0.98 |\n| T cell | 223 | 0.94 | 0.94 | 0.95 | 0.93 | 0.00 | 0.97 | 0.99 | 0.97 | 0.99 |\n| myeloid dendritic cell | 223 | 0.85 | 0.84 | 0.91 | 0.92 | 0.00 | 0.69 | 0.86 | 0.88 | 0.93 |\n| pulmonary interstitial fibroblast | 201 | 0.97 | 0.98 | 0.97 | 0.99 | 0.00 | 0.97 | 1.00 | 0.99 | 0.99 |\n| basophil | 121 | 0.94 | 0.89 | 0.97 | 0.92 | 0.00 | 0.83 | 0.98 | 0.99 | 0.99 |\n| regulatory T cell | 111 | 0.00 | 0.62 | 0.70 | 0.59 | 0.00 | 0.93 | 0.98 | 1.00 | 0.91 |\n| smooth muscle cell of the pulmonary artery | 84 | 0.79 | 0.90 | 0.94 | 0.58 | 0.00 | 0.95 | 0.97 | 0.92 | 0.94 |\n| plasmacytoid dendritic cell | 67 | 0.86 | 0.93 | 0.87 | 0.89 | 0.00 | 0.87 | 0.99 | 0.99 | 0.96 |\n| pericyte | 55 | 0.99 | 0.99 | 0.96 | 0.96 | 0.00 | 0.96 | 0.97 | 1.00 | 0.99 |\n| ciliated columnar cell of tracheobronchial tree | 47 | 0.86 | 0.99 | 0.98 | 0.96 | 0.00 | 0.99 | 0.97 | 1.00 | 0.99 |\n| plasma cell | 48 | 0.91 | 0.96 | 0.95 | 0.97 | 0.00 | 1.00 | 0.99 | 0.98 | 1.00 |\n| dendritic cell | 42 | 0.00 | 0.73 | 0.78 | 0.83 | 0.00 | 0.66 | 0.85 | 0.91 | 0.89 |\n| endothelial cell of lymphatic vessel | 37 | 0.97 | 0.97 | 1.00 | 0.89 | 0.00 | 0.88 | 1.00 | 0.99 | 1.00 |\n| club cell | 11 | 0.03 | 0.42 | 0.11 | 0.09 | 0.00 | 0.14 | 0.19 | 0.17 | 0.15 |\n| lung neuroendocrine cell | 4 | 0.00 | 0.00 | 1.00 | 0.73 | 0.00 | 0.89 | 1.00 | 1.00 | 1.00 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| classical monocyte | 782 | 0.94 | 0.92 | 0.94 | 0.95 | 0.00 | 0.91 | 0.90 | 0.92 | 0.96 |\n| bronchial smooth muscle cell | 228 | 0.98 | 0.98 | 0.98 | 0.94 | 0.00 | 0.96 | 0.98 | 0.97 | 0.99 |\n| intermediate monocyte | 174 | 0.72 | 0.51 | 0.71 | 0.76 | 0.00 | 0.77 | 0.64 | 0.70 | 0.80 |\n| fibroblast of lung | 149 | 0.97 | 0.99 | 0.99 | 0.95 | 0.00 | 0.97 | 0.99 | 0.98 | 0.98 |\n| B cell | 151 | 0.99 | 1.00 | 0.98 | 1.00 | 0.00 | 0.99 | 0.99 | 1.00 | 1.00 |\n| alveolar macrophage | 142 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| natural killer cell | 128 | 0.99 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |\n| lung macrophage | 121 | 0.97 | 0.90 | 0.95 | 0.98 | 0.00 | 0.94 | 0.97 | 0.94 | 0.97 |\n| non-classical monocyte | 95 | 0.95 | 0.84 | 0.88 | 0.92 | 0.00 | 0.94 | 0.94 | 0.95 | 0.96 |\n| CD8-positive, alpha-beta T cell | 85 | 0.88 | 0.88 | 0.85 | 0.80 | 0.00 | 0.83 | 0.87 | 0.89 | 0.90 |\n| neutrophil | 70 | 1.00 | 0.96 | 0.98 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 53 | 0.75 | 0.82 | 0.76 | 0.73 | 0.00 | 0.83 | 0.82 | 0.82 | 0.85 |\n| adventitial cell | 54 | 0.93 | 0.97 | 0.95 | 0.84 | 0.00 | 0.92 | 0.96 | 0.95 | 0.95 |\n| mature NK T cell | 43 | 0.84 | 0.90 | 0.92 | 0.85 | 0.00 | 0.88 | 0.92 | 0.85 | 0.93 |\n| vein endothelial cell | 32 | 0.94 | 0.92 | 0.92 | 0.68 | 0.00 | 0.90 | 0.94 | 0.87 | 0.94 |\n| T cell | 28 | 0.96 | 0.96 | 0.96 | 0.93 | 0.00 | 0.97 | 0.95 | 0.96 | 0.98 |\n| myeloid dendritic cell | 23 | 0.94 | 0.94 | 0.92 | 0.85 | 0.00 | 0.66 | 0.87 | 0.85 | 0.94 |\n| pulmonary interstitial fibroblast | 18 | 1.00 | 1.00 | 0.97 | 0.97 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |\n| basophil | 9 | 1.00 | 0.80 | 0.89 | 0.71 | 0.00 | 0.76 | 0.78 | 0.82 | 0.89 |\n| regulatory T cell | 13 | 0.56 | 0.70 | 0.47 | 0.52 | 0.00 | 0.92 | 0.87 | 0.76 | 0.76 |\n| smooth muscle cell of the pulmonary artery | 14 | 0.83 | 0.88 | 0.92 | 0.48 | 0.00 | 0.65 | 0.86 | 0.89 | 0.92 |\n| plasmacytoid dendritic cell | 8 | 0.88 | 0.93 | 0.93 | 0.86 | 0.00 | 0.89 | 1.00 | 1.00 | 0.93 |\n| pericyte | 6 | 1.00 | 1.00 | 1.00 | 0.91 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| ciliated columnar cell of tracheobronchial tree | 7 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| plasma cell | 1 | 0.67 | 1.00 | 1.00 | 1.00 | 0.00 | 0.50 | 0.67 | 1.00 | 1.00 |\n| dendritic cell | 3 | 0.33 | 0.40 | 0.50 | 0.33 | 0.00 | 0.22 | 0.57 | 0.25 | 0.40 |\n| endothelial cell of lymphatic vessel | 4 | 1.00 | 1.00 | 0.86 | 0.89 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| club cell | 4 | 0.47 | 0.00 | 0.47 | 0.57 | 0.00 | 0.47 | 0.50 | 0.47 | 0.47 |\n| lung neuroendocrine cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
+    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| classical monocyte | 7140 | 0.94 | 0.92 | 0.96 | 0.97 | 0.00 | 0.92 | 0.92 | 0.92 | 0.97 |\n| bronchial smooth muscle cell | 2111 | 0.98 | 0.99 | 0.99 | 0.96 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |\n| intermediate monocyte | 1575 | 0.72 | 0.49 | 0.79 | 0.85 | 0.00 | 0.78 | 0.72 | 0.74 | 0.87 |\n| fibroblast of lung | 1374 | 0.97 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| B cell | 1350 | 1.00 | 1.00 | 0.99 | 1.00 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| alveolar macrophage | 1224 | 0.99 | 0.97 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| natural killer cell | 1065 | 0.99 | 0.99 | 0.96 | 0.99 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| lung macrophage | 1036 | 0.97 | 0.92 | 0.98 | 0.97 | 0.00 | 0.96 | 0.97 | 0.96 | 0.98 |\n| non-classical monocyte | 915 | 0.96 | 0.84 | 0.93 | 0.97 | 0.00 | 0.97 | 0.96 | 0.97 | 0.98 |\n| CD8-positive, alpha-beta T cell | 785 | 0.89 | 0.90 | 0.89 | 0.86 | 0.00 | 0.93 | 0.97 | 0.97 | 0.95 |\n| neutrophil | 482 | 1.00 | 0.96 | 0.98 | 1.00 | 0.00 | 0.95 | 1.00 | 0.98 | 1.00 |\n| CD4-positive, alpha-beta T cell | 498 | 0.78 | 0.80 | 0.85 | 0.77 | 0.00 | 0.88 | 0.97 | 0.97 | 0.92 |\n| adventitial cell | 472 | 0.92 | 0.93 | 0.95 | 0.95 | 0.00 | 0.95 | 0.98 | 0.98 | 0.97 |\n| mature NK T cell | 377 | 0.86 | 0.86 | 0.86 | 0.85 | 0.00 | 0.90 | 0.98 | 0.98 | 0.94 |\n| vein endothelial cell | 288 | 0.94 | 0.96 | 0.95 | 0.81 | 0.00 | 0.92 | 0.95 | 0.94 | 0.97 |\n| T cell | 223 | 0.94 | 0.94 | 0.95 | 0.93 | 0.00 | 0.96 | 0.98 | 0.97 | 0.98 |\n| myeloid dendritic cell | 222 | 0.89 | 0.85 | 0.92 | 0.91 | 0.00 | 0.73 | 0.88 | 0.91 | 0.93 |\n| pulmonary interstitial fibroblast | 204 | 1.00 | 0.97 | 0.97 | 0.98 | 0.00 | 0.97 | 1.00 | 0.99 | 0.99 |\n| basophil | 121 | 0.97 | 0.89 | 0.96 | 0.94 | 0.00 | 0.93 | 0.98 | 0.98 | 1.00 |\n| regulatory T cell | 110 | 0.44 | 0.64 | 0.70 | 0.61 | 0.00 | 0.89 | 1.00 | 0.99 | 0.91 |\n| smooth muscle cell of the pulmonary artery | 84 | 0.82 | 0.90 | 0.94 | 0.60 | 0.00 | 0.79 | 0.98 | 0.97 | 0.96 |\n| plasmacytoid dendritic cell | 67 | 0.86 | 0.93 | 0.88 | 0.91 | 0.00 | 0.93 | 0.99 | 0.96 | 0.98 |\n| pericyte | 55 | 0.99 | 0.99 | 0.96 | 0.95 | 0.00 | 0.97 | 0.97 | 1.00 | 0.99 |\n| ciliated columnar cell of tracheobronchial tree | 50 | 0.99 | 0.98 | 0.98 | 0.95 | 0.00 | 0.97 | 0.98 | 1.00 | 0.98 |\n| plasma cell | 48 | 0.95 | 0.98 | 0.97 | 0.95 | 0.00 | 0.96 | 1.00 | 0.98 | 1.00 |\n| dendritic cell | 42 | 0.45 | 0.73 | 0.82 | 0.81 | 0.00 | 0.47 | 0.93 | 0.90 | 0.84 |\n| endothelial cell of lymphatic vessel | 37 | 0.97 | 0.97 | 0.99 | 0.89 | 0.00 | 0.99 | 1.00 | 1.00 | 0.99 |\n| club cell | 11 | 0.13 | 0.27 | 0.11 | 0.18 | 0.00 | 0.15 | 0.17 | 0.17 | 0.15 |\n| lung neuroendocrine cell | 4 | 0.00 | 0.40 | 0.86 | 0.89 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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         "ENSMUSG00000020914",
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         "ENSMUSG00000021367",
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