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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| fibroblast | 642 | 0.98 | 0.95 | 0.98 | 0.97 | 0.00 | 0.96 | 0.96 | 0.97 | 0.99 |\n| CD4-positive, alpha-beta T cell | 573 | 0.90 | 0.91 | 0.89 | 0.86 | 0.00 | 0.79 | 0.92 | 0.91 | 0.93 |\n| mononuclear phagocyte | 525 | 0.96 | 0.90 | 0.97 | 0.91 | 0.00 | 0.90 | 0.93 | 0.94 | 0.97 |\n| plasma cell | 426 | 0.99 | 0.98 | 0.94 | 0.95 | 0.00 | 0.96 | 0.99 | 0.99 | 0.99 |\n| B cell | 212 | 0.92 | 0.93 | 0.94 | 0.92 | 0.00 | 0.94 | 0.94 | 0.93 | 0.95 |\n| epithelial cell | 165 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.96 | 0.98 | 0.99 | 0.99 |\n| CD8-positive, alpha-beta T cell | 168 | 0.74 | 0.72 | 0.75 | 0.64 | 0.00 | 0.62 | 0.74 | 0.73 | 0.76 |\n| macrophage | 109 | 0.79 | 0.15 | 0.81 | 0.48 | 0.00 | 0.66 | 0.77 | 0.79 | 0.82 |\n| monocyte | 109 | 0.88 | 0.89 | 0.91 | 0.89 | 0.00 | 0.89 | 0.83 | 0.81 | 0.91 |\n| mast cell | 98 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.96 | 1.00 | 0.97 | 0.99 |\n| neutrophil | 96 | 0.99 | 1.00 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 1.00 | 0.99 |\n| tissue-resident macrophage | 59 | 0.83 | 0.10 | 0.80 | 0.79 | 0.00 | 0.78 | 0.71 | 0.80 | 0.89 |\n| endothelial cell of lymphatic vessel | 58 | 0.98 | 0.96 | 0.99 | 0.91 | 0.00 | 0.92 | 1.00 | 0.95 | 0.97 |\n| regulatory T cell | 23 | 0.44 | 0.00 | 0.15 | 0.06 | 0.00 | 0.33 | 0.72 | 0.88 | 0.56 |\n| natural killer cell | 11 | 0.65 | 0.56 | 0.54 | 0.61 | 0.00 | 0.63 | 0.63 | 0.62 | 0.58 |\n| mature NK T cell | 13 | 0.00 | 0.25 | 0.48 | 0.18 | 0.00 | 0.61 | 0.71 | 0.62 | 0.50 |\n| T cell | 11 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.67 | 0.25 | 0.29 |\n| interstitial cell of Cajal | 6 | 0.86 | 0.00 | 1.00 | 0.50 | 0.00 | 0.60 | 1.00 | 1.00 | 1.00 |\n| smooth muscle cell | 3 | 0.60 | 0.80 | 0.67 | 0.00 | 0.00 | 0.67 | 0.40 | 0.46 | 0.60 |\n| enteroendocrine 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| fibroblast | 5903 | 0.98 | 0.95 | 0.99 | 0.98 | 0.00 | 0.96 | 0.97 | 0.98 | 0.99 |\n| CD4-positive, alpha-beta T cell | 5211 | 0.91 | 0.91 | 0.93 | 0.92 | 0.00 | 0.86 | 0.93 | 0.94 | 0.95 |\n| mononuclear phagocyte | 4811 | 0.96 | 0.89 | 0.97 | 0.95 | 0.00 | 0.94 | 0.95 | 0.95 | 0.97 |\n| plasma cell | 3757 | 0.99 | 0.96 | 0.97 | 0.97 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |\n| B cell | 1969 | 0.94 | 0.90 | 0.95 | 0.93 | 0.00 | 0.93 | 0.95 | 0.95 | 0.95 |\n| epithelial cell | 1436 | 0.98 | 0.97 | 0.99 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |\n| CD8-positive, alpha-beta T cell | 1418 | 0.75 | 0.76 | 0.82 | 0.76 | 0.00 | 0.75 | 0.82 | 0.83 | 0.84 |\n| macrophage | 954 | 0.79 | 0.13 | 0.85 | 0.77 | 0.00 | 0.73 | 0.84 | 0.87 | 0.87 |\n| monocyte | 945 | 0.86 | 0.80 | 0.89 | 0.89 | 0.00 | 0.87 | 0.86 | 0.87 | 0.90 |\n| mast cell | 870 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.96 | 0.99 | 0.98 | 0.98 |\n| neutrophil | 832 | 1.00 | 0.94 | 0.99 | 0.98 | 0.00 | 0.98 | 1.00 | 0.99 | 1.00 |\n| tissue-resident macrophage | 588 | 0.83 | 0.05 | 0.89 | 0.87 | 0.00 | 0.75 | 0.77 | 0.83 | 0.89 |\n| endothelial cell of lymphatic vessel | 492 | 0.99 | 0.93 | 0.99 | 0.96 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |\n| regulatory T cell | 206 | 0.45 | 0.00 | 0.52 | 0.07 | 0.00 | 0.43 | 0.67 | 0.92 | 0.73 |\n| natural killer cell | 112 | 0.71 | 0.58 | 0.80 | 0.71 | 0.00 | 0.75 | 0.89 | 0.89 | 0.86 |\n| mature NK T cell | 74 | 0.00 | 0.03 | 0.66 | 0.29 | 0.00 | 0.69 | 0.85 | 0.83 | 0.87 |\n| T cell | 65 | 0.00 | 0.00 | 0.23 | 0.11 | 0.00 | 0.39 | 0.77 | 0.70 | 0.87 |\n| interstitial cell of Cajal | 65 | 0.79 | 0.00 | 0.91 | 0.85 | 0.00 | 0.70 | 0.94 | 0.93 | 0.93 |\n| smooth muscle cell | 24 | 0.69 | 0.14 | 0.77 | 0.46 | 0.00 | 0.53 | 0.86 | 0.89 | 0.79 |\n| enteroendocrine cell | 25 | 0.66 | 0.27 | 0.96 | 0.78 | 0.00 | 0.66 | 0.98 | 0.98 | 0.94 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| fibroblast | 645 | 0.96 | 0.96 | 0.98 | 0.98 | 0.00 | 0.95 | 0.96 | 0.96 | 0.98 |\n| CD4-positive, alpha-beta T cell | 568 | 0.90 | 0.91 | 0.88 | 0.86 | 0.00 | 0.85 | 0.90 | 0.92 | 0.92 |\n| mononuclear phagocyte | 530 | 0.96 | 0.89 | 0.96 | 0.89 | 0.00 | 0.93 | 0.94 | 0.93 | 0.96 |\n| plasma cell | 425 | 0.99 | 0.97 | 0.95 | 0.99 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |\n| B cell | 212 | 0.93 | 0.92 | 0.94 | 0.94 | 0.00 | 0.95 | 0.93 | 0.93 | 0.96 |\n| epithelial cell | 162 | 0.98 | 0.96 | 0.98 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |\n| CD8-positive, alpha-beta T cell | 161 | 0.70 | 0.73 | 0.71 | 0.63 | 0.00 | 0.69 | 0.72 | 0.75 | 0.73 |\n| macrophage | 112 | 0.80 | 0.19 | 0.81 | 0.47 | 0.00 | 0.75 | 0.77 | 0.78 | 0.82 |\n| monocyte | 115 | 0.89 | 0.88 | 0.89 | 0.82 | 0.00 | 0.79 | 0.84 | 0.80 | 0.89 |\n| mast cell | 102 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| neutrophil | 94 | 1.00 | 1.00 | 0.99 | 0.98 | 0.00 | 0.98 | 1.00 | 0.99 | 1.00 |\n| tissue-resident macrophage | 60 | 0.74 | 0.09 | 0.85 | 0.76 | 0.00 | 0.70 | 0.70 | 0.75 | 0.87 |\n| endothelial cell of lymphatic vessel | 58 | 0.98 | 0.97 | 0.97 | 0.92 | 0.00 | 0.94 | 0.97 | 0.93 | 0.97 |\n| regulatory T cell | 22 | 0.36 | 0.00 | 0.24 | 0.06 | 0.00 | 0.45 | 0.69 | 0.89 | 0.48 |\n| natural killer cell | 9 | 0.50 | 0.35 | 0.50 | 0.50 | 0.00 | 0.59 | 0.54 | 0.54 | 0.56 |\n| mature NK T cell | 13 | 0.41 | 0.00 | 0.61 | 0.00 | 0.00 | 0.73 | 0.69 | 0.71 | 0.64 |\n| T cell | 10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 0.47 | 0.32 | 0.00 |\n| interstitial cell of Cajal | 5 | 1.00 | 0.00 | 1.00 | 0.73 | 0.00 | 1.00 | 1.00 | 0.91 | 1.00 |\n| smooth muscle cell | 4 | 0.55 | 0.57 | 0.40 | 0.00 | 0.00 | 0.80 | 0.50 | 0.60 | 0.60 |\n| enteroendocrine 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| fibroblast | 5900 | 0.97 | 0.95 | 0.99 | 0.98 | 0.00 | 0.96 | 0.97 | 0.97 | 0.99 |\n| CD4-positive, alpha-beta T cell | 5216 | 0.91 | 0.91 | 0.93 | 0.93 | 0.00 | 0.90 | 0.92 | 0.94 | 0.95 |\n| mononuclear phagocyte | 4806 | 0.96 | 0.89 | 0.97 | 0.95 | 0.00 | 0.95 | 0.95 | 0.95 | 0.97 |\n| plasma cell | 3758 | 0.98 | 0.96 | 0.97 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| B cell | 1969 | 0.94 | 0.90 | 0.95 | 0.94 | 0.00 | 0.94 | 0.95 | 0.95 | 0.96 |\n| epithelial cell | 1439 | 0.98 | 0.97 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| CD8-positive, alpha-beta T cell | 1425 | 0.74 | 0.76 | 0.84 | 0.77 | 0.00 | 0.79 | 0.82 | 0.83 | 0.84 |\n| macrophage | 951 | 0.83 | 0.15 | 0.86 | 0.78 | 0.00 | 0.84 | 0.84 | 0.87 | 0.88 |\n| monocyte | 939 | 0.86 | 0.80 | 0.90 | 0.87 | 0.00 | 0.81 | 0.86 | 0.86 | 0.90 |\n| mast cell | 866 | 0.98 | 0.96 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.98 |\n| neutrophil | 834 | 0.99 | 0.93 | 0.99 | 0.98 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| tissue-resident macrophage | 587 | 0.74 | 0.05 | 0.88 | 0.87 | 0.00 | 0.72 | 0.76 | 0.81 | 0.89 |\n| endothelial cell of lymphatic vessel | 492 | 0.99 | 0.95 | 0.99 | 0.96 | 0.00 | 0.98 | 0.99 | 0.95 | 0.99 |\n| regulatory T cell | 207 | 0.34 | 0.00 | 0.44 | 0.18 | 0.00 | 0.54 | 0.66 | 0.91 | 0.62 |\n| natural killer cell | 114 | 0.65 | 0.58 | 0.79 | 0.67 | 0.00 | 0.85 | 0.92 | 0.88 | 0.86 |\n| mature NK T cell | 74 | 0.36 | 0.05 | 0.66 | 0.34 | 0.00 | 0.68 | 0.85 | 0.83 | 0.86 |\n| T cell | 66 | 0.00 | 0.00 | 0.14 | 0.08 | 0.00 | 0.44 | 0.76 | 0.74 | 0.86 |\n| interstitial cell of Cajal | 66 | 0.81 | 0.00 | 0.89 | 0.88 | 0.00 | 0.89 | 0.94 | 0.91 | 0.91 |\n| smooth muscle cell | 23 | 0.66 | 0.24 | 0.73 | 0.47 | 0.00 | 0.71 | 0.87 | 0.84 | 0.81 |\n| enteroendocrine cell | 25 | 0.00 | 0.20 | 0.93 | 0.86 | 0.00 | 0.64 | 0.91 | 0.93 | 0.93 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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         "ENSG00000001497",
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         "ENSG00000010295",
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         "ENSG00000071127",
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