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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| macrophage | 1630 | 0.96 | 0.97 | 0.98 | 0.98 | 0.00 | 0.95 | 0.97 | 0.95 | 0.98 |\n| pulmonary alveolar type 2 cell | 1138 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.96 | 0.98 | 0.97 | 0.98 |\n| capillary endothelial cell | 701 | 0.97 | 0.95 | 0.97 | 0.97 | 0.00 | 0.97 | 0.96 | 0.96 | 0.98 |\n| basal cell | 403 | 0.92 | 0.91 | 0.94 | 0.94 | 0.00 | 0.91 | 0.94 | 0.94 | 0.95 |\n| pulmonary alveolar type 1 cell | 301 | 0.99 | 0.98 | 0.97 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| intermediate monocyte | 272 | 0.64 | 0.63 | 0.69 | 0.67 | 0.00 | 0.59 | 0.78 | 0.82 | 0.78 |\n| CD4-positive, alpha-beta T cell | 213 | 0.88 | 0.89 | 0.86 | 0.83 | 0.00 | 0.89 | 0.88 | 0.88 | 0.90 |\n| CD8-positive, alpha-beta T cell | 206 | 0.85 | 0.86 | 0.81 | 0.77 | 0.00 | 0.85 | 0.84 | 0.86 | 0.88 |\n| endothelial cell of artery | 165 | 0.79 | 0.80 | 0.82 | 0.81 | 0.00 | 0.81 | 0.72 | 0.79 | 0.84 |\n| club cell | 173 | 0.79 | 0.82 | 0.86 | 0.84 | 0.00 | 0.76 | 0.85 | 0.83 | 0.87 |\n| classical monocyte | 153 | 0.57 | 0.57 | 0.63 | 0.60 | 0.00 | 0.66 | 0.71 | 0.88 | 0.77 |\n| vein endothelial cell | 143 | 0.80 | 0.80 | 0.83 | 0.84 | 0.00 | 0.82 | 0.79 | 0.85 | 0.87 |\n| basophil | 147 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.98 | 1.00 | 0.99 |\n| lung ciliated cell | 136 | 0.97 | 0.99 | 0.99 | 0.97 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |\n| alveolar adventitial fibroblast | 120 | 0.84 | 0.87 | 0.83 | 0.92 | 0.00 | 0.92 | 0.90 | 0.91 | 0.92 |\n| respiratory goblet cell | 109 | 0.77 | 0.82 | 0.84 | 0.81 | 0.00 | 0.75 | 0.83 | 0.82 | 0.83 |\n| natural killer cell | 104 | 0.86 | 0.89 | 0.86 | 0.87 | 0.00 | 0.90 | 0.89 | 0.86 | 0.90 |\n| pericyte | 82 | 0.78 | 0.89 | 0.91 | 0.94 | 0.00 | 0.89 | 0.92 | 0.91 | 0.93 |\n| B cell | 69 | 0.99 | 0.99 | 0.99 | 0.96 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |\n| adventitial cell | 59 | 0.81 | 0.82 | 0.75 | 0.89 | 0.00 | 0.82 | 0.84 | 0.87 | 0.87 |\n| non-classical monocyte | 55 | 0.34 | 0.14 | 0.36 | 0.14 | 0.00 | 0.40 | 0.51 | 0.82 | 0.53 |\n| monocyte | 50 | 0.37 | 0.20 | 0.44 | 0.31 | 0.00 | 0.42 | 0.47 | 0.72 | 0.51 |\n| neutrophil | 39 | 0.96 | 0.97 | 0.94 | 0.99 | 0.00 | 0.97 | 0.96 | 0.87 | 0.97 |\n| endothelial cell of lymphatic vessel | 28 | 0.95 | 0.98 | 0.98 | 0.97 | 0.00 | 0.93 | 0.98 | 0.97 | 0.98 |\n| bronchial smooth muscle cell | 25 | 0.00 | 0.56 | 0.64 | 0.33 | 0.00 | 0.71 | 0.69 | 0.74 | 0.69 |\n| mature NK T cell | 27 | 0.00 | 0.14 | 0.32 | 0.24 | 0.00 | 0.50 | 0.58 | 0.35 | 0.42 |\n| plasma cell | 12 | 0.71 | 0.74 | 0.87 | 0.92 | 0.00 | 0.89 | 0.92 | 0.96 | 0.92 |\n| vascular associated smooth muscle cell | 14 | 0.00 | 0.57 | 0.58 | 0.65 | 0.00 | 0.68 | 0.90 | 0.67 | 0.80 |\n| myeloid dendritic cell | 6 | 0.00 | 0.00 | 0.73 | 0.91 | 0.00 | 0.77 | 0.91 | 0.92 | 0.80 |\n| pulmonary ionocyte | 1 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |\n| mesothelial cell | 1 | 0.00 | 0.50 | 0.50 | 0.50 | 0.00 | 0.29 | 0.33 | 0.50 | 0.50 |\n| serous cell of epithelium of bronchus | 2 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.25 | 0.80 | 0.67 | 0.00 |\n| mast 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| macrophage | 14856 | 0.96 | 0.98 | 0.98 | 0.98 | 0.00 | 0.95 | 0.97 | 0.95 | 0.98 |\n| pulmonary alveolar type 2 cell | 10456 | 0.97 | 0.97 | 0.99 | 0.98 | 0.00 | 0.95 | 0.98 | 0.97 | 0.98 |\n| capillary endothelial cell | 6542 | 0.97 | 0.95 | 0.98 | 0.98 | 0.00 | 0.96 | 0.96 | 0.96 | 0.98 |\n| basal cell | 3612 | 0.93 | 0.93 | 0.97 | 0.96 | 0.00 | 0.93 | 0.96 | 0.95 | 0.97 |\n| pulmonary alveolar type 1 cell | 2815 | 0.97 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.97 | 0.98 |\n| intermediate monocyte | 2513 | 0.64 | 0.62 | 0.78 | 0.78 | 0.00 | 0.64 | 0.82 | 0.86 | 0.84 |\n| CD4-positive, alpha-beta T cell | 1911 | 0.88 | 0.87 | 0.90 | 0.88 | 0.00 | 0.89 | 0.91 | 0.92 | 0.93 |\n| CD8-positive, alpha-beta T cell | 1692 | 0.85 | 0.83 | 0.87 | 0.84 | 0.00 | 0.86 | 0.88 | 0.90 | 0.91 |\n| endothelial cell of artery | 1589 | 0.79 | 0.80 | 0.86 | 0.84 | 0.00 | 0.81 | 0.82 | 0.83 | 0.86 |\n| club cell | 1574 | 0.83 | 0.82 | 0.92 | 0.89 | 0.00 | 0.77 | 0.88 | 0.87 | 0.91 |\n| classical monocyte | 1416 | 0.60 | 0.57 | 0.71 | 0.72 | 0.00 | 0.71 | 0.82 | 0.92 | 0.84 |\n| vein endothelial cell | 1193 | 0.82 | 0.81 | 0.88 | 0.87 | 0.00 | 0.85 | 0.86 | 0.88 | 0.88 |\n| basophil | 1175 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| lung ciliated cell | 1073 | 0.96 | 0.97 | 0.99 | 0.99 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| alveolar adventitial fibroblast | 993 | 0.87 | 0.85 | 0.89 | 0.94 | 0.00 | 0.94 | 0.97 | 0.97 | 0.96 |\n| respiratory goblet cell | 931 | 0.81 | 0.86 | 0.90 | 0.89 | 0.00 | 0.80 | 0.89 | 0.88 | 0.91 |\n| natural killer cell | 915 | 0.91 | 0.92 | 0.92 | 0.90 | 0.00 | 0.94 | 0.96 | 0.96 | 0.96 |\n| pericyte | 657 | 0.79 | 0.88 | 0.94 | 0.94 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| B cell | 594 | 0.98 | 0.97 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| adventitial cell | 522 | 0.81 | 0.80 | 0.83 | 0.90 | 0.00 | 0.90 | 0.96 | 0.96 | 0.94 |\n| non-classical monocyte | 472 | 0.26 | 0.08 | 0.36 | 0.31 | 0.00 | 0.51 | 0.70 | 0.84 | 0.66 |\n| monocyte | 456 | 0.40 | 0.21 | 0.54 | 0.54 | 0.00 | 0.54 | 0.76 | 0.83 | 0.79 |\n| neutrophil | 332 | 0.96 | 0.95 | 0.97 | 0.95 | 0.00 | 0.96 | 0.98 | 0.93 | 0.98 |\n| endothelial cell of lymphatic vessel | 287 | 0.96 | 0.98 | 0.98 | 0.97 | 0.00 | 0.95 | 0.99 | 0.99 | 0.98 |\n| bronchial smooth muscle cell | 195 | 0.00 | 0.56 | 0.74 | 0.66 | 0.00 | 0.86 | 0.90 | 0.94 | 0.94 |\n| mature NK T cell | 136 | 0.00 | 0.14 | 0.50 | 0.29 | 0.00 | 0.68 | 0.79 | 0.86 | 0.88 |\n| plasma cell | 136 | 0.67 | 0.80 | 0.95 | 0.94 | 0.00 | 0.95 | 0.98 | 0.94 | 0.96 |\n| vascular associated smooth muscle cell | 117 | 0.00 | 0.47 | 0.72 | 0.66 | 0.00 | 0.82 | 0.98 | 0.98 | 0.96 |\n| myeloid dendritic cell | 27 | 0.00 | 0.06 | 0.84 | 0.83 | 0.00 | 0.44 | 0.95 | 0.93 | 0.93 |\n| pulmonary ionocyte | 24 | 0.00 | 0.78 | 0.98 | 0.84 | 0.00 | 0.83 | 0.94 | 0.96 | 0.98 |\n| plasmacytoid dendritic cell | 18 | 0.00 | 0.00 | 1.00 | 0.92 | 0.00 | 0.92 | 1.00 | 1.00 | 1.00 |\n| mesothelial cell | 17 | 0.00 | 0.83 | 0.81 | 0.79 | 0.00 | 0.42 | 0.87 | 0.92 | 0.83 |\n| serous cell of epithelium of bronchus | 13 | 0.00 | 0.27 | 0.60 | 0.53 | 0.00 | 0.55 | 0.93 | 0.96 | 0.70 |\n| mast cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.60 | 1.00 | 1.00 | 0.50 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| macrophage | 1632 | 0.96 | 0.97 | 0.98 | 0.98 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |\n| pulmonary alveolar type 2 cell | 1146 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |\n| capillary endothelial cell | 698 | 0.97 | 0.95 | 0.98 | 0.97 | 0.00 | 0.97 | 0.96 | 0.96 | 0.97 |\n| basal cell | 411 | 0.92 | 0.93 | 0.94 | 0.93 | 0.00 | 0.94 | 0.93 | 0.93 | 0.95 |\n| pulmonary alveolar type 1 cell | 302 | 0.98 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| intermediate monocyte | 278 | 0.64 | 0.62 | 0.67 | 0.69 | 0.00 | 0.54 | 0.77 | 0.84 | 0.77 |\n| 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 |\n| 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 |\n| endothelial cell of artery | 158 | 0.79 | 0.78 | 0.84 | 0.75 | 0.00 | 0.81 | 0.77 | 0.79 | 0.82 |\n| club cell | 181 | 0.82 | 0.82 | 0.85 | 0.83 | 0.00 | 0.83 | 0.85 | 0.83 | 0.87 |\n| classical monocyte | 154 | 0.58 | 0.57 | 0.61 | 0.61 | 0.00 | 0.57 | 0.73 | 0.89 | 0.74 |\n| vein endothelial cell | 142 | 0.81 | 0.80 | 0.87 | 0.79 | 0.00 | 0.84 | 0.81 | 0.84 | 0.85 |\n| basophil | 145 | 0.97 | 0.99 | 0.99 | 1.00 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| lung ciliated cell | 134 | 0.97 | 0.99 | 0.99 | 0.99 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| alveolar adventitial fibroblast | 117 | 0.85 | 0.86 | 0.86 | 0.90 | 0.00 | 0.90 | 0.91 | 0.91 | 0.94 |\n| respiratory goblet cell | 107 | 0.76 | 0.82 | 0.83 | 0.80 | 0.00 | 0.84 | 0.83 | 0.83 | 0.84 |\n| natural killer cell | 104 | 0.87 | 0.88 | 0.87 | 0.85 | 0.00 | 0.90 | 0.87 | 0.89 | 0.90 |\n| pericyte | 76 | 0.79 | 0.86 | 0.88 | 0.89 | 0.00 | 0.90 | 0.90 | 0.92 | 0.92 |\n| B cell | 67 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |\n| adventitial cell | 61 | 0.68 | 0.83 | 0.81 | 0.85 | 0.00 | 0.85 | 0.87 | 0.88 | 0.90 |\n| non-classical monocyte | 55 | 0.32 | 0.11 | 0.34 | 0.06 | 0.00 | 0.36 | 0.56 | 0.77 | 0.55 |\n| monocyte | 51 | 0.42 | 0.33 | 0.38 | 0.46 | 0.00 | 0.32 | 0.48 | 0.72 | 0.58 |\n| neutrophil | 35 | 0.92 | 0.97 | 0.94 | 0.94 | 0.00 | 0.96 | 0.97 | 0.89 | 0.96 |\n| endothelial cell of lymphatic vessel | 32 | 0.96 | 0.97 | 0.92 | 0.96 | 0.00 | 0.94 | 0.97 | 0.97 | 0.98 |\n| bronchial smooth muscle cell | 24 | 0.49 | 0.48 | 0.69 | 0.51 | 0.00 | 0.54 | 0.64 | 0.78 | 0.73 |\n| mature NK T cell | 27 | 0.00 | 0.25 | 0.31 | 0.21 | 0.00 | 0.56 | 0.48 | 0.51 | 0.45 |\n| plasma cell | 12 | 0.87 | 0.85 | 0.92 | 0.96 | 0.00 | 0.92 | 0.89 | 0.92 | 0.96 |\n| vascular associated smooth muscle cell | 18 | 0.53 | 0.52 | 0.47 | 0.64 | 0.00 | 0.79 | 0.76 | 0.75 | 0.73 |\n| myeloid dendritic cell | 6 | 0.00 | 0.00 | 0.83 | 0.80 | 0.00 | 0.77 | 0.67 | 0.92 | 0.91 |\n| pulmonary ionocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 0.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 1.00 | 0.67 | 0.00 | 0.40 | 1.00 | 1.00 | 1.00 |\n| mesothelial cell | 1 | 0.00 | 0.50 | 0.50 | 0.50 | 0.00 | 0.40 | 0.40 | 0.50 | 0.50 |\n| 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 |\n| mast 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| macrophage | 14854 | 0.96 | 0.98 | 0.98 | 0.98 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |\n| pulmonary alveolar type 2 cell | 10448 | 0.97 | 0.97 | 0.99 | 0.98 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |\n| capillary endothelial cell | 6545 | 0.97 | 0.96 | 0.98 | 0.98 | 0.00 | 0.97 | 0.96 | 0.96 | 0.98 |\n| basal cell | 3604 | 0.92 | 0.94 | 0.96 | 0.96 | 0.00 | 0.94 | 0.95 | 0.95 | 0.97 |\n| pulmonary alveolar type 1 cell | 2814 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.97 | 0.98 |\n| intermediate monocyte | 2507 | 0.62 | 0.62 | 0.78 | 0.78 | 0.00 | 0.63 | 0.81 | 0.87 | 0.83 |\n| 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 |\n| 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 |\n| endothelial cell of artery | 1596 | 0.78 | 0.79 | 0.86 | 0.85 | 0.00 | 0.82 | 0.82 | 0.83 | 0.86 |\n| club cell | 1566 | 0.82 | 0.82 | 0.91 | 0.90 | 0.00 | 0.86 | 0.88 | 0.86 | 0.91 |\n| classical monocyte | 1415 | 0.60 | 0.56 | 0.72 | 0.71 | 0.00 | 0.71 | 0.81 | 0.93 | 0.84 |\n| vein endothelial cell | 1194 | 0.81 | 0.81 | 0.88 | 0.86 | 0.00 | 0.85 | 0.86 | 0.89 | 0.88 |\n| basophil | 1177 | 0.97 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| lung ciliated cell | 1075 | 0.96 | 0.97 | 0.99 | 0.99 | 0.00 | 0.95 | 0.98 | 0.98 | 0.98 |\n| alveolar adventitial fibroblast | 996 | 0.87 | 0.85 | 0.89 | 0.94 | 0.00 | 0.93 | 0.96 | 0.97 | 0.96 |\n| respiratory goblet cell | 933 | 0.80 | 0.86 | 0.89 | 0.89 | 0.00 | 0.87 | 0.88 | 0.88 | 0.91 |\n| natural killer cell | 915 | 0.90 | 0.91 | 0.93 | 0.93 | 0.00 | 0.94 | 0.95 | 0.96 | 0.96 |\n| pericyte | 663 | 0.78 | 0.89 | 0.94 | 0.92 | 0.00 | 0.95 | 0.98 | 0.98 | 0.97 |\n| B cell | 596 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| adventitial cell | 520 | 0.75 | 0.80 | 0.83 | 0.91 | 0.00 | 0.91 | 0.95 | 0.96 | 0.95 |\n| non-classical monocyte | 472 | 0.26 | 0.08 | 0.34 | 0.30 | 0.00 | 0.45 | 0.71 | 0.80 | 0.68 |\n| monocyte | 455 | 0.43 | 0.27 | 0.53 | 0.53 | 0.00 | 0.49 | 0.76 | 0.83 | 0.77 |\n| neutrophil | 336 | 0.93 | 0.97 | 0.98 | 0.96 | 0.00 | 0.97 | 0.99 | 0.95 | 0.99 |\n| endothelial cell of lymphatic vessel | 283 | 0.96 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.99 | 0.98 |\n| bronchial smooth muscle cell | 196 | 0.50 | 0.55 | 0.77 | 0.60 | 0.00 | 0.80 | 0.91 | 0.95 | 0.91 |\n| mature NK T cell | 136 | 0.00 | 0.15 | 0.53 | 0.40 | 0.00 | 0.70 | 0.83 | 0.91 | 0.91 |\n| plasma cell | 136 | 0.81 | 0.83 | 0.95 | 0.94 | 0.00 | 0.94 | 0.97 | 0.94 | 0.98 |\n| vascular associated smooth muscle cell | 113 | 0.48 | 0.50 | 0.75 | 0.61 | 0.00 | 0.83 | 0.95 | 0.95 | 0.94 |\n| myeloid dendritic cell | 27 | 0.00 | 0.12 | 0.84 | 0.73 | 0.00 | 0.77 | 0.93 | 0.90 | 0.96 |\n| pulmonary ionocyte | 24 | 0.00 | 0.89 | 0.98 | 0.88 | 0.00 | 0.79 | 0.96 | 0.94 | 0.96 |\n| plasmacytoid dendritic cell | 18 | 0.00 | 0.00 | 0.95 | 0.95 | 0.00 | 0.86 | 0.97 | 0.97 | 0.97 |\n| mesothelial cell | 17 | 0.00 | 0.79 | 0.81 | 0.77 | 0.00 | 0.60 | 0.92 | 0.87 | 0.83 |\n| 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 |\n| mast cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 1.00 | 0.86 | 0.50 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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         "ENSG00000004848",
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         "ENSG00000034971",
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         "ENSG00000078725",
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