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OnClass.data-00000-of-00001

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OnClass.npz

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accuracies.json

@@ -1,4 +1,4 @@
 {
-    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| basal cell | 1640 | 0.86 | 0.90 | 0.93 | 0.91 | 0.00 | 0.87 | 0.87 | 0.88 | 0.91 |\n| stratified squamous epithelial cell | 1174 | 0.83 | 0.89 | 0.91 | 0.89 | 0.00 | 0.84 | 0.84 | 0.86 | 0.89 |\n| CD4-positive, alpha-beta T cell | 153 | 0.69 | 0.73 | 0.71 | 0.64 | 0.00 | 0.59 | 0.65 | 0.73 | 0.74 |\n| fibroblast | 179 | 0.97 | 0.96 | 0.97 | 0.96 | 0.00 | 0.96 | 0.96 | 0.95 | 0.97 |\n| B cell | 120 | 0.97 | 0.96 | 0.96 | 0.89 | 0.00 | 0.94 | 0.97 | 0.97 | 0.97 |\n| endothelial cell | 131 | 0.99 | 0.98 | 0.99 | 0.97 | 0.00 | 0.98 | 0.98 | 0.97 | 0.98 |\n| CD8-positive, alpha-beta T cell | 125 | 0.75 | 0.77 | 0.74 | 0.61 | 0.00 | 0.70 | 0.70 | 0.79 | 0.78 |\n| salivary gland cell | 84 | 0.87 | 0.13 | 0.88 | 0.84 | 0.00 | 0.67 | 0.86 | 0.85 | 0.86 |\n| mural cell | 66 | 0.95 | 0.93 | 0.97 | 0.93 | 0.00 | 0.95 | 0.95 | 0.94 | 0.95 |\n| macrophage | 54 | 0.75 | 0.82 | 0.79 | 0.81 | 0.00 | 0.80 | 0.78 | 0.76 | 0.80 |\n| myoepithelial cell | 30 | 0.87 | 0.00 | 0.92 | 0.88 | 0.00 | 0.77 | 0.88 | 0.86 | 0.87 |\n| tongue muscle cell | 15 | 0.90 | 0.90 | 0.90 | 0.84 | 0.00 | 0.76 | 0.90 | 0.84 | 0.87 |\n| T cell | 20 | 0.26 | 0.00 | 0.19 | 0.00 | 0.00 | 0.32 | 0.34 | 0.30 | 0.31 |\n| neutrophil | 16 | 1.00 | 1.00 | 0.97 | 0.94 | 0.00 | 0.97 | 1.00 | 0.97 | 1.00 |\n| monocyte | 12 | 0.57 | 0.62 | 0.46 | 0.40 | 0.00 | 0.55 | 0.48 | 0.54 | 0.59 |\n| plasma cell | 9 | 0.88 | 0.80 | 0.94 | 0.31 | 0.00 | 0.82 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of lymphatic vessel | 8 | 0.80 | 0.86 | 0.86 | 0.71 | 0.00 | 0.71 | 0.78 | 0.71 | 0.75 |\n| regulatory T cell | 10 | 0.42 | 0.46 | 0.67 | 0.00 | 0.00 | 0.43 | 0.52 | 0.82 | 0.59 |\n| mast cell | 10 | 0.87 | 0.82 | 0.90 | 0.80 | 0.00 | 0.87 | 0.87 | 0.86 | 0.87 |\n| Schwann cell | 5 | 0.62 | 0.67 | 0.80 | 0.55 | 0.00 | 0.50 | 0.80 | 0.60 | 0.73 |\n| taste receptor cell | 2 | 0.67 | 0.67 | 1.00 | 0.67 | 0.00 | 0.33 | 0.67 | 0.00 | 0.67 |\n| myeloid dendritic cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 0.40 | 0.00 | 0.00 |\n| natural killer cell | 1 | 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| basal cell | 14623 | 0.87 | 0.89 | 0.96 | 0.94 | 0.00 | 0.88 | 0.89 | 0.89 | 0.92 |\n| stratified squamous epithelial cell | 11141 | 0.85 | 0.90 | 0.95 | 0.93 | 0.00 | 0.86 | 0.87 | 0.88 | 0.91 |\n| CD4-positive, alpha-beta T cell | 1434 | 0.74 | 0.71 | 0.84 | 0.77 | 0.00 | 0.77 | 0.82 | 0.85 | 0.87 |\n| fibroblast | 1352 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |\n| B cell | 1130 | 0.98 | 0.94 | 0.99 | 0.94 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| endothelial cell | 1090 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.98 |\n| CD8-positive, alpha-beta T cell | 982 | 0.77 | 0.74 | 0.83 | 0.70 | 0.00 | 0.82 | 0.84 | 0.88 | 0.86 |\n| salivary gland cell | 764 | 0.89 | 0.08 | 0.94 | 0.90 | 0.00 | 0.71 | 0.91 | 0.91 | 0.93 |\n| mural cell | 552 | 0.92 | 0.91 | 0.95 | 0.93 | 0.00 | 0.95 | 0.96 | 0.97 | 0.95 |\n| macrophage | 516 | 0.79 | 0.85 | 0.91 | 0.87 | 0.00 | 0.90 | 0.94 | 0.93 | 0.93 |\n| myoepithelial cell | 240 | 0.82 | 0.00 | 0.91 | 0.88 | 0.00 | 0.75 | 0.89 | 0.88 | 0.91 |\n| tongue muscle cell | 187 | 0.85 | 0.83 | 0.90 | 0.84 | 0.00 | 0.84 | 0.98 | 0.98 | 0.95 |\n| T cell | 174 | 0.47 | 0.00 | 0.54 | 0.28 | 0.00 | 0.66 | 0.77 | 0.79 | 0.83 |\n| neutrophil | 138 | 0.93 | 0.97 | 0.99 | 0.96 | 0.00 | 0.90 | 0.98 | 0.99 | 0.98 |\n| monocyte | 127 | 0.58 | 0.54 | 0.75 | 0.71 | 0.00 | 0.75 | 0.90 | 0.95 | 0.92 |\n| plasma cell | 106 | 0.93 | 0.86 | 0.99 | 0.64 | 0.00 | 0.89 | 1.00 | 0.98 | 1.00 |\n| endothelial cell of lymphatic vessel | 89 | 0.94 | 0.95 | 0.97 | 0.91 | 0.00 | 0.89 | 0.97 | 0.97 | 0.96 |\n| regulatory T cell | 82 | 0.55 | 0.02 | 0.69 | 0.11 | 0.00 | 0.71 | 0.88 | 0.88 | 0.88 |\n| mast cell | 66 | 0.97 | 0.99 | 0.99 | 0.88 | 0.00 | 0.96 | 0.98 | 0.94 | 0.98 |\n| Schwann cell | 30 | 0.57 | 0.55 | 0.72 | 0.74 | 0.00 | 0.75 | 1.00 | 0.98 | 0.87 |\n| taste receptor cell | 30 | 0.82 | 0.29 | 0.89 | 0.72 | 0.00 | 0.40 | 0.97 | 0.58 | 0.95 |\n| myeloid dendritic cell | 18 | 0.00 | 0.00 | 0.20 | 0.00 | 0.00 | 0.73 | 1.00 | 0.97 | 0.71 |\n| natural killer cell | 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.59 | 0.93 | 0.93 | 0.60 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| basal cell | 1655 | 0.86 | 0.89 | 0.92 | 0.90 | 0.00 | 0.85 | 0.88 | 0.88 | 0.91 |\n| stratified squamous epithelial cell | 1166 | 0.84 | 0.89 | 0.90 | 0.87 | 0.00 | 0.84 | 0.85 | 0.85 | 0.89 |\n| CD4-positive, alpha-beta T cell | 155 | 0.68 | 0.72 | 0.72 | 0.62 | 0.00 | 0.71 | 0.66 | 0.69 | 0.75 |\n| fibroblast | 173 | 0.97 | 0.97 | 0.98 | 0.96 | 0.00 | 0.96 | 0.96 | 0.96 | 0.96 |\n| B cell | 121 | 0.97 | 0.97 | 0.97 | 0.89 | 0.00 | 0.95 | 0.97 | 0.97 | 0.97 |\n| endothelial cell | 133 | 0.99 | 0.99 | 0.99 | 0.97 | 0.00 | 0.97 | 0.97 | 0.97 | 0.98 |\n| CD8-positive, alpha-beta T cell | 125 | 0.75 | 0.74 | 0.74 | 0.62 | 0.00 | 0.78 | 0.73 | 0.79 | 0.78 |\n| salivary gland cell | 87 | 0.89 | 0.13 | 0.91 | 0.82 | 0.00 | 0.67 | 0.85 | 0.89 | 0.89 |\n| mural cell | 61 | 0.95 | 0.93 | 0.97 | 0.94 | 0.00 | 0.94 | 0.95 | 0.92 | 0.95 |\n| macrophage | 50 | 0.81 | 0.79 | 0.81 | 0.69 | 0.00 | 0.74 | 0.83 | 0.80 | 0.81 |\n| myoepithelial cell | 26 | 0.79 | 0.00 | 0.87 | 0.82 | 0.00 | 0.78 | 0.83 | 0.84 | 0.88 |\n| tongue muscle cell | 15 | 0.76 | 0.79 | 0.81 | 0.83 | 0.00 | 0.82 | 0.75 | 0.83 | 0.80 |\n| T cell | 20 | 0.37 | 0.00 | 0.19 | 0.00 | 0.00 | 0.30 | 0.39 | 0.32 | 0.33 |\n| neutrophil | 18 | 0.92 | 1.00 | 1.00 | 0.89 | 0.00 | 0.97 | 1.00 | 0.95 | 1.00 |\n| monocyte | 12 | 0.65 | 0.55 | 0.50 | 0.27 | 0.00 | 0.50 | 0.64 | 0.52 | 0.64 |\n| plasma cell | 10 | 0.95 | 0.75 | 0.95 | 0.46 | 0.00 | 1.00 | 1.00 | 0.95 | 1.00 |\n| endothelial cell of lymphatic vessel | 8 | 0.80 | 0.86 | 0.80 | 0.80 | 0.00 | 0.80 | 0.80 | 0.80 | 0.80 |\n| regulatory T cell | 9 | 0.29 | 0.33 | 0.29 | 0.00 | 0.00 | 0.55 | 0.53 | 0.76 | 0.53 |\n| mast cell | 11 | 0.88 | 0.88 | 0.92 | 0.60 | 0.00 | 0.85 | 0.88 | 0.92 | 0.88 |\n| Schwann cell | 4 | 0.60 | 0.75 | 0.75 | 0.67 | 0.00 | 0.67 | 0.75 | 0.67 | 0.67 |\n| taste receptor cell | 2 | 0.67 | 0.67 | 0.67 | 0.67 | 0.00 | 0.25 | 1.00 | 0.50 | 0.67 |\n| myeloid dendritic cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| natural killer 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| basal cell | 14608 | 0.87 | 0.89 | 0.96 | 0.94 | 0.00 | 0.87 | 0.89 | 0.90 | 0.93 |\n| stratified squamous epithelial cell | 11147 | 0.86 | 0.90 | 0.95 | 0.93 | 0.00 | 0.87 | 0.87 | 0.88 | 0.92 |\n| CD4-positive, alpha-beta T cell | 1432 | 0.75 | 0.73 | 0.84 | 0.76 | 0.00 | 0.81 | 0.82 | 0.87 | 0.87 |\n| fibroblast | 1358 | 0.96 | 0.97 | 0.98 | 0.97 | 0.00 | 0.96 | 0.98 | 0.97 | 0.98 |\n| B cell | 1129 | 0.99 | 0.96 | 0.99 | 0.94 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| endothelial cell | 1088 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| CD8-positive, alpha-beta T cell | 982 | 0.77 | 0.74 | 0.84 | 0.69 | 0.00 | 0.82 | 0.83 | 0.88 | 0.85 |\n| salivary gland cell | 761 | 0.88 | 0.07 | 0.93 | 0.88 | 0.00 | 0.69 | 0.91 | 0.92 | 0.92 |\n| mural cell | 557 | 0.92 | 0.91 | 0.95 | 0.94 | 0.00 | 0.94 | 0.97 | 0.97 | 0.95 |\n| macrophage | 520 | 0.80 | 0.85 | 0.91 | 0.84 | 0.00 | 0.90 | 0.96 | 0.94 | 0.95 |\n| myoepithelial cell | 244 | 0.82 | 0.00 | 0.92 | 0.88 | 0.00 | 0.78 | 0.88 | 0.88 | 0.91 |\n| tongue muscle cell | 187 | 0.86 | 0.83 | 0.90 | 0.81 | 0.00 | 0.88 | 0.96 | 0.98 | 0.94 |\n| T cell | 174 | 0.49 | 0.00 | 0.51 | 0.32 | 0.00 | 0.65 | 0.75 | 0.80 | 0.83 |\n| neutrophil | 136 | 0.86 | 0.97 | 0.98 | 0.93 | 0.00 | 0.94 | 0.98 | 0.97 | 0.97 |\n| monocyte | 127 | 0.65 | 0.51 | 0.75 | 0.68 | 0.00 | 0.70 | 0.95 | 0.97 | 0.95 |\n| plasma cell | 105 | 0.94 | 0.84 | 0.99 | 0.55 | 0.00 | 0.97 | 1.00 | 0.98 | 1.00 |\n| endothelial cell of lymphatic vessel | 89 | 0.93 | 0.93 | 0.97 | 0.94 | 0.00 | 0.91 | 0.98 | 0.97 | 0.97 |\n| regulatory T cell | 83 | 0.49 | 0.02 | 0.65 | 0.07 | 0.00 | 0.83 | 0.85 | 0.88 | 0.83 |\n| mast cell | 65 | 0.97 | 0.98 | 0.98 | 0.71 | 0.00 | 0.96 | 0.97 | 0.96 | 0.98 |\n| Schwann cell | 31 | 0.56 | 0.57 | 0.70 | 0.55 | 0.00 | 0.83 | 0.98 | 0.95 | 0.85 |\n| taste receptor cell | 30 | 0.82 | 0.50 | 0.89 | 0.72 | 0.00 | 0.28 | 0.98 | 0.68 | 0.97 |\n| myeloid dendritic cell | 17 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.34 | 1.00 | 1.00 | 0.69 |\n| natural killer cell | 8 | 0.00 | 0.00 | 0.22 | 0.00 | 0.00 | 0.52 | 0.94 | 1.00 | 0.40 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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         "ENSG00000018408",
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