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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| kidney proximal convoluted tubule epithelial cell | 433 | 0.91 | 0.89 | 0.85 | 0.85 | 0.00 | 0.83 | 0.90 | 0.91 | 0.91 |\n| B cell | 296 | 0.97 | 0.97 | 0.96 | 0.98 | 0.00 | 0.98 | 0.97 | 0.97 | 0.97 |\n| epithelial cell of proximal tubule | 318 | 0.87 | 0.89 | 0.78 | 0.75 | 0.00 | 0.79 | 0.86 | 0.87 | 0.88 |\n| kidney loop of Henle thick ascending limb epithelial cell | 137 | 0.91 | 0.94 | 0.92 | 0.90 | 0.00 | 0.93 | 0.91 | 0.92 | 0.94 |\n| lymphocyte | 167 | 0.95 | 0.84 | 0.94 | 0.96 | 0.00 | 0.94 | 0.96 | 0.95 | 0.97 |\n| macrophage | 147 | 0.98 | 0.99 | 0.97 | 0.98 | 0.00 | 0.98 | 0.97 | 0.97 | 0.99 |\n| T cell | 125 | 0.99 | 0.98 | 0.98 | 0.96 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |\n| kidney collecting duct principal cell | 82 | 0.93 | 0.98 | 0.96 | 0.96 | 0.00 | 0.94 | 0.96 | 0.96 | 0.97 |\n| kidney distal convoluted tubule epithelial cell | 92 | 0.95 | 0.97 | 0.95 | 0.94 | 0.00 | 0.96 | 0.96 | 0.95 | 0.96 |\n| plasmatocyte | 44 | 0.91 | 0.98 | 0.98 | 0.95 | 0.00 | 0.97 | 0.96 | 0.95 | 0.99 |\n| brush cell | 47 | 0.92 | 0.95 | 0.91 | 0.92 | 0.00 | 0.95 | 0.91 | 0.95 | 0.95 |\n| kidney cortex artery cell | 37 | 0.78 | 0.83 | 0.76 | 0.62 | 0.00 | 0.80 | 0.87 | 0.78 | 0.83 |\n| plasma cell | 32 | 0.71 | 0.40 | 0.70 | 0.68 | 0.00 | 0.75 | 0.72 | 0.77 | 0.72 |\n| mesangial cell | 31 | 0.89 | 0.98 | 0.93 | 0.95 | 0.00 | 0.92 | 0.98 | 0.97 | 0.98 |\n| kidney loop of Henle ascending limb epithelial cell | 19 | 0.00 | 0.55 | 0.22 | 0.00 | 0.00 | 0.58 | 0.53 | 0.62 | 0.44 |\n| kidney capillary endothelial cell | 18 | 0.26 | 0.49 | 0.24 | 0.16 | 0.00 | 0.24 | 0.27 | 0.27 | 0.27 |\n| fibroblast | 13 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| kidney proximal straight tubule epithelial cell | 10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.38 | 0.41 | 0.18 |\n| natural killer cell | 7 | 1.00 | 0.92 | 0.92 | 0.25 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |\n| kidney collecting duct epithelial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| leukocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| kidney 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| kidney proximal convoluted tubule epithelial cell | 4027 | 0.92 | 0.90 | 0.89 | 0.89 | 0.00 | 0.85 | 0.92 | 0.94 | 0.95 |\n| B cell | 2828 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| epithelial cell of proximal tubule | 2735 | 0.89 | 0.90 | 0.83 | 0.83 | 0.00 | 0.82 | 0.89 | 0.91 | 0.92 |\n| kidney loop of Henle thick ascending limb epithelial cell | 1417 | 0.92 | 0.93 | 0.95 | 0.93 | 0.00 | 0.96 | 0.97 | 0.98 | 0.97 |\n| lymphocyte | 1369 | 0.95 | 0.78 | 0.97 | 0.97 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| macrophage | 1260 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |\n| T cell | 1234 | 0.98 | 0.98 | 0.98 | 0.97 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| kidney collecting duct principal cell | 707 | 0.92 | 0.97 | 0.96 | 0.96 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |\n| kidney distal convoluted tubule epithelial cell | 652 | 0.89 | 0.94 | 0.94 | 0.93 | 0.00 | 0.97 | 0.99 | 0.99 | 0.96 |\n| plasmatocyte | 452 | 0.89 | 0.94 | 0.94 | 0.94 | 0.00 | 0.96 | 0.96 | 0.98 | 0.97 |\n| brush cell | 367 | 0.90 | 0.92 | 0.94 | 0.95 | 0.00 | 0.94 | 0.95 | 0.97 | 0.96 |\n| kidney cortex artery cell | 344 | 0.80 | 0.84 | 0.82 | 0.67 | 0.00 | 0.84 | 0.85 | 0.81 | 0.84 |\n| plasma cell | 293 | 0.85 | 0.62 | 0.91 | 0.90 | 0.00 | 0.89 | 0.95 | 0.93 | 0.96 |\n| mesangial cell | 230 | 0.88 | 0.96 | 0.97 | 0.94 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| kidney loop of Henle ascending limb epithelial cell | 182 | 0.00 | 0.36 | 0.49 | 0.30 | 0.00 | 0.80 | 0.80 | 0.88 | 0.71 |\n| kidney capillary endothelial cell | 143 | 0.24 | 0.41 | 0.25 | 0.23 | 0.00 | 0.26 | 0.27 | 0.28 | 0.27 |\n| fibroblast | 148 | 0.98 | 0.99 | 0.97 | 0.96 | 0.00 | 0.99 | 1.00 | 1.00 | 0.99 |\n| kidney proximal straight tubule epithelial cell | 85 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.68 | 0.66 | 0.58 | 0.69 |\n| natural killer cell | 59 | 0.79 | 0.80 | 0.85 | 0.63 | 0.00 | 0.83 | 0.92 | 0.93 | 0.88 |\n| kidney collecting duct epithelial cell | 25 | 0.00 | 0.07 | 0.08 | 0.19 | 0.00 | 0.89 | 1.00 | 1.00 | 0.39 |\n| leukocyte | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.73 | 1.00 | 1.00 | 0.00 |\n| kidney cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 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| kidney proximal convoluted tubule epithelial cell | 434 | 0.90 | 0.89 | 0.85 | 0.84 | 0.00 | 0.86 | 0.87 | 0.91 | 0.92 |\n| B cell | 307 | 0.98 | 0.98 | 0.97 | 0.98 | 0.00 | 0.99 | 0.98 | 0.98 | 0.98 |\n| epithelial cell of proximal tubule | 302 | 0.87 | 0.89 | 0.78 | 0.76 | 0.00 | 0.83 | 0.84 | 0.88 | 0.90 |\n| kidney loop of Henle thick ascending limb epithelial cell | 145 | 0.92 | 0.91 | 0.91 | 0.91 | 0.00 | 0.93 | 0.93 | 0.95 | 0.93 |\n| lymphocyte | 152 | 0.95 | 0.82 | 0.95 | 0.95 | 0.00 | 0.95 | 0.96 | 0.95 | 0.96 |\n| macrophage | 142 | 0.98 | 0.99 | 0.97 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| T cell | 128 | 1.00 | 0.98 | 0.98 | 0.97 | 0.00 | 0.99 | 1.00 | 0.97 | 0.99 |\n| kidney collecting duct principal cell | 89 | 0.96 | 0.97 | 0.96 | 0.96 | 0.00 | 0.95 | 0.97 | 0.95 | 0.97 |\n| kidney distal convoluted tubule epithelial cell | 90 | 0.95 | 0.96 | 0.94 | 0.97 | 0.00 | 0.96 | 0.96 | 0.93 | 0.96 |\n| plasmatocyte | 49 | 0.94 | 0.93 | 0.95 | 0.95 | 0.00 | 0.92 | 0.94 | 0.92 | 0.95 |\n| brush cell | 48 | 0.91 | 0.92 | 0.86 | 0.90 | 0.00 | 0.91 | 0.88 | 0.92 | 0.93 |\n| kidney cortex artery cell | 37 | 0.76 | 0.82 | 0.80 | 0.70 | 0.00 | 0.86 | 0.79 | 0.79 | 0.83 |\n| plasma cell | 36 | 0.78 | 0.51 | 0.69 | 0.75 | 0.00 | 0.85 | 0.79 | 0.82 | 0.83 |\n| mesangial cell | 31 | 0.92 | 0.98 | 0.97 | 0.94 | 0.00 | 0.98 | 0.98 | 0.98 | 1.00 |\n| kidney loop of Henle ascending limb epithelial cell | 22 | 0.40 | 0.37 | 0.29 | 0.20 | 0.00 | 0.50 | 0.64 | 0.71 | 0.44 |\n| fibroblast | 14 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |\n| kidney capillary endothelial cell | 16 | 0.24 | 0.45 | 0.25 | 0.23 | 0.00 | 0.25 | 0.27 | 0.27 | 0.26 |\n| kidney proximal straight tubule epithelial cell | 8 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.21 | 0.31 | 0.00 |\n| natural killer cell | 7 | 1.00 | 0.73 | 0.83 | 0.44 | 0.00 | 1.00 | 1.00 | 0.92 | 1.00 |\n| kidney collecting duct epithelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| leukocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| kidney 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| kidney proximal convoluted tubule epithelial cell | 4026 | 0.91 | 0.90 | 0.89 | 0.90 | 0.00 | 0.87 | 0.92 | 0.94 | 0.94 |\n| B cell | 2817 | 0.99 | 0.98 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| epithelial cell of proximal tubule | 2751 | 0.88 | 0.90 | 0.84 | 0.85 | 0.00 | 0.87 | 0.89 | 0.90 | 0.92 |\n| kidney loop of Henle thick ascending limb epithelial cell | 1409 | 0.93 | 0.93 | 0.95 | 0.93 | 0.00 | 0.97 | 0.97 | 0.98 | 0.96 |\n| lymphocyte | 1384 | 0.94 | 0.79 | 0.97 | 0.97 | 0.00 | 0.95 | 0.97 | 0.97 | 0.98 |\n| macrophage | 1265 | 0.96 | 0.98 | 0.97 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| T cell | 1231 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| kidney collecting duct principal cell | 700 | 0.96 | 0.97 | 0.97 | 0.96 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |\n| kidney distal convoluted tubule epithelial cell | 654 | 0.94 | 0.94 | 0.95 | 0.93 | 0.00 | 0.97 | 0.99 | 0.99 | 0.96 |\n| plasmatocyte | 447 | 0.92 | 0.94 | 0.93 | 0.95 | 0.00 | 0.95 | 0.96 | 0.97 | 0.96 |\n| brush cell | 366 | 0.92 | 0.93 | 0.93 | 0.96 | 0.00 | 0.93 | 0.95 | 0.97 | 0.97 |\n| kidney cortex artery cell | 344 | 0.79 | 0.84 | 0.82 | 0.79 | 0.00 | 0.84 | 0.78 | 0.82 | 0.84 |\n| plasma cell | 289 | 0.88 | 0.60 | 0.87 | 0.90 | 0.00 | 0.90 | 0.91 | 0.89 | 0.95 |\n| mesangial cell | 230 | 0.89 | 0.96 | 0.97 | 0.94 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |\n| kidney loop of Henle ascending limb epithelial cell | 179 | 0.20 | 0.35 | 0.48 | 0.25 | 0.00 | 0.82 | 0.83 | 0.90 | 0.66 |\n| fibroblast | 147 | 0.98 | 0.98 | 0.96 | 0.98 | 0.00 | 0.95 | 1.00 | 0.99 | 0.99 |\n| kidney capillary endothelial cell | 145 | 0.24 | 0.39 | 0.26 | 0.23 | 0.00 | 0.26 | 0.29 | 0.28 | 0.27 |\n| kidney proximal straight tubule epithelial cell | 87 | 0.00 | 0.00 | 0.02 | 0.00 | 0.00 | 0.47 | 0.66 | 0.62 | 0.68 |\n| natural killer cell | 59 | 0.79 | 0.77 | 0.83 | 0.63 | 0.00 | 0.82 | 0.94 | 0.93 | 0.89 |\n| kidney collecting duct epithelial cell | 24 | 0.00 | 0.00 | 0.08 | 0.27 | 0.00 | 0.89 | 1.00 | 0.98 | 0.40 |\n| leukocyte | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 0.00 |\n| kidney cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 1.00 | 1.00 | 0.67 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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         "ENSMUSG00000001657",
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         "ENSMUSG00000003813",
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