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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| CD4-positive, alpha-beta T cell | 745 | 0.79 | 0.84 | 0.84 | 0.78 | 0.00 | 0.67 | 0.74 | 0.78 | 0.85 |\n| CD4-positive, alpha-beta thymocyte | 439 | 0.72 | 0.51 | 0.74 | 0.65 | 0.00 | 0.69 | 0.64 | 0.71 | 0.76 |\n| B cell | 450 | 1.00 | 1.00 | 0.99 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| thymic fibroblast type 2 | 372 | 0.82 | 0.88 | 0.89 | 0.86 | 0.00 | 0.91 | 0.89 | 0.89 | 0.92 |\n| thymic fibroblast type 1 | 345 | 0.81 | 0.86 | 0.88 | 0.85 | 0.00 | 0.90 | 0.88 | 0.88 | 0.91 |\n| CD8-positive, alpha-beta T cell | 289 | 0.81 | 0.85 | 0.86 | 0.82 | 0.00 | 0.82 | 0.82 | 0.85 | 0.85 |\n| capillary endothelial cell | 272 | 0.82 | 0.87 | 0.89 | 0.86 | 0.00 | 0.81 | 0.82 | 0.81 | 0.86 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 257 | 0.49 | 0.45 | 0.49 | 0.32 | 0.00 | 0.50 | 0.45 | 0.49 | 0.56 |\n| smooth muscle cell | 227 | 0.95 | 0.97 | 0.97 | 0.97 | 0.00 | 0.99 | 0.99 | 0.97 | 0.98 |\n| vein endothelial cell | 213 | 0.86 | 0.85 | 0.88 | 0.85 | 0.00 | 0.83 | 0.84 | 0.83 | 0.87 |\n| plasma cell | 137 | 1.00 | 0.99 | 0.97 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of artery | 84 | 0.85 | 0.93 | 0.93 | 0.87 | 0.00 | 0.91 | 0.90 | 0.89 | 0.93 |\n| macrophage | 85 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| CD8-positive, alpha-beta thymocyte | 71 | 0.63 | 0.73 | 0.78 | 0.39 | 0.00 | 0.78 | 0.69 | 0.76 | 0.82 |\n| thymocyte | 49 | 0.44 | 0.63 | 0.83 | 0.42 | 0.00 | 0.75 | 0.70 | 0.77 | 0.82 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 37 | 0.44 | 0.49 | 0.57 | 0.00 | 0.00 | 0.31 | 0.54 | 0.61 | 0.62 |\n| natural killer cell | 45 | 0.93 | 0.94 | 0.94 | 0.87 | 0.00 | 0.91 | 0.97 | 0.95 | 0.94 |\n| endothelial cell of lymphatic vessel | 35 | 1.00 | 1.00 | 1.00 | 0.99 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| fibroblast | 22 | 0.41 | 0.26 | 0.26 | 0.39 | 0.00 | 0.67 | 0.79 | 0.76 | 0.81 |\n| vascular associated smooth muscle cell | 12 | 0.61 | 0.00 | 0.27 | 0.14 | 0.00 | 0.96 | 0.92 | 0.76 | 0.74 |\n| mesothelial cell | 16 | 0.93 | 0.90 | 0.94 | 0.80 | 0.00 | 0.86 | 0.91 | 0.88 | 0.91 |\n| erythrocyte | 18 | 0.89 | 0.97 | 0.91 | 0.97 | 0.00 | 0.97 | 0.97 | 0.97 | 0.94 |\n| neuro-medullary thymic epithelial cell | 14 | 0.96 | 0.96 | 0.96 | 0.96 | 0.00 | 1.00 | 1.00 | 0.96 | 1.00 |\n| neutrophil | 13 | 0.70 | 0.83 | 0.88 | 0.92 | 0.00 | 0.81 | 0.93 | 0.85 | 0.93 |\n| hematopoietic precursor cell | 10 | 0.80 | 0.57 | 0.95 | 0.86 | 0.00 | 0.80 | 0.89 | 0.90 | 0.89 |\n| myo-medullary thymic epithelial cell | 5 | 0.77 | 0.80 | 0.91 | 0.91 | 0.00 | 0.91 | 0.91 | 0.91 | 0.91 |\n| medullary thymic epithelial cell | 7 | 1.00 | 0.86 | 0.92 | 0.40 | 0.00 | 0.93 | 0.92 | 1.00 | 1.00 |\n| monocyte | 2 | 0.00 | 0.00 | 1.00 | 0.67 | 0.00 | 0.80 | 0.67 | 0.40 | 0.67 |\n| mast cell | 2 | 1.00 | 1.00 | 1.00 | 0.67 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |\n| fast muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| T follicular helper cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| endothelial 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| CD4-positive, alpha-beta T cell | 6381 | 0.77 | 0.82 | 0.88 | 0.83 | 0.00 | 0.70 | 0.74 | 0.78 | 0.86 |\n| CD4-positive, alpha-beta thymocyte | 4124 | 0.72 | 0.45 | 0.84 | 0.80 | 0.00 | 0.76 | 0.69 | 0.75 | 0.81 |\n| B cell | 4012 | 1.00 | 0.99 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| thymic fibroblast type 2 | 3833 | 0.87 | 0.90 | 0.95 | 0.93 | 0.00 | 0.92 | 0.93 | 0.92 | 0.95 |\n| thymic fibroblast type 1 | 2925 | 0.83 | 0.86 | 0.93 | 0.90 | 0.00 | 0.90 | 0.90 | 0.90 | 0.93 |\n| CD8-positive, alpha-beta T cell | 2528 | 0.80 | 0.84 | 0.90 | 0.86 | 0.00 | 0.82 | 0.83 | 0.84 | 0.87 |\n| capillary endothelial cell | 2349 | 0.84 | 0.85 | 0.94 | 0.90 | 0.00 | 0.87 | 0.90 | 0.89 | 0.92 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 2266 | 0.50 | 0.41 | 0.66 | 0.59 | 0.00 | 0.55 | 0.50 | 0.56 | 0.65 |\n| smooth muscle cell | 1998 | 0.95 | 0.94 | 0.99 | 0.98 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| vein endothelial cell | 1835 | 0.85 | 0.82 | 0.93 | 0.88 | 0.00 | 0.88 | 0.89 | 0.89 | 0.92 |\n| plasma cell | 1441 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of artery | 689 | 0.89 | 0.93 | 0.96 | 0.91 | 0.00 | 0.92 | 0.97 | 0.95 | 0.96 |\n| macrophage | 685 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| CD8-positive, alpha-beta thymocyte | 601 | 0.61 | 0.71 | 0.82 | 0.60 | 0.00 | 0.82 | 0.77 | 0.79 | 0.85 |\n| thymocyte | 406 | 0.57 | 0.63 | 0.83 | 0.57 | 0.00 | 0.84 | 0.83 | 0.88 | 0.92 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 397 | 0.44 | 0.43 | 0.71 | 0.10 | 0.00 | 0.54 | 0.66 | 0.76 | 0.78 |\n| natural killer cell | 383 | 0.92 | 0.91 | 0.94 | 0.89 | 0.00 | 0.92 | 0.97 | 0.97 | 0.96 |\n| endothelial cell of lymphatic vessel | 336 | 0.97 | 0.97 | 0.98 | 0.96 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |\n| fibroblast | 250 | 0.61 | 0.06 | 0.94 | 0.85 | 0.00 | 0.94 | 0.92 | 0.88 | 0.96 |\n| vascular associated smooth muscle cell | 229 | 0.63 | 0.07 | 0.96 | 0.82 | 0.00 | 0.97 | 0.97 | 0.96 | 0.98 |\n| mesothelial cell | 159 | 0.94 | 0.91 | 0.96 | 0.94 | 0.00 | 0.97 | 0.97 | 0.98 | 0.98 |\n| erythrocyte | 134 | 0.89 | 0.94 | 0.94 | 0.94 | 0.00 | 0.95 | 0.98 | 0.95 | 0.98 |\n| neuro-medullary thymic epithelial cell | 121 | 0.92 | 0.92 | 0.92 | 0.92 | 0.00 | 0.90 | 1.00 | 0.99 | 0.98 |\n| neutrophil | 108 | 0.60 | 0.73 | 0.90 | 0.87 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |\n| hematopoietic precursor cell | 82 | 0.74 | 0.20 | 0.86 | 0.85 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| myo-medullary thymic epithelial cell | 72 | 0.79 | 0.87 | 0.96 | 0.95 | 0.00 | 0.97 | 0.99 | 1.00 | 0.97 |\n| medullary thymic epithelial cell | 36 | 0.84 | 0.70 | 0.87 | 0.69 | 0.00 | 0.97 | 1.00 | 1.00 | 0.99 |\n| monocyte | 24 | 0.00 | 0.00 | 0.88 | 0.63 | 0.00 | 0.86 | 0.98 | 1.00 | 0.98 |\n| mast cell | 22 | 0.88 | 0.81 | 0.87 | 0.73 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| fast muscle cell | 21 | 0.00 | 0.14 | 0.98 | 0.95 | 0.00 | 1.00 | 1.00 | 1.00 | 0.98 |\n| T follicular helper cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.92 | 1.00 | 0.91 |\n| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.20 | 0.80 | 0.80 | 1.00 |\n| endothelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 0.00 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| CD4-positive, alpha-beta T cell | 745 | 0.77 | 0.85 | 0.84 | 0.79 | 0.00 | 0.73 | 0.73 | 0.78 | 0.85 |\n| CD4-positive, alpha-beta thymocyte | 424 | 0.66 | 0.53 | 0.74 | 0.67 | 0.00 | 0.63 | 0.63 | 0.71 | 0.73 |\n| B cell | 453 | 1.00 | 0.99 | 0.99 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| thymic fibroblast type 2 | 381 | 0.87 | 0.90 | 0.89 | 0.90 | 0.00 | 0.92 | 0.89 | 0.91 | 0.94 |\n| thymic fibroblast type 1 | 337 | 0.88 | 0.87 | 0.89 | 0.88 | 0.00 | 0.92 | 0.89 | 0.90 | 0.93 |\n| CD8-positive, alpha-beta T cell | 290 | 0.81 | 0.86 | 0.86 | 0.81 | 0.00 | 0.86 | 0.84 | 0.86 | 0.87 |\n| capillary endothelial cell | 275 | 0.83 | 0.86 | 0.90 | 0.83 | 0.00 | 0.83 | 0.84 | 0.84 | 0.88 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 261 | 0.49 | 0.46 | 0.49 | 0.39 | 0.00 | 0.53 | 0.40 | 0.52 | 0.57 |\n| smooth muscle cell | 223 | 0.98 | 0.96 | 0.97 | 0.97 | 0.00 | 0.98 | 0.99 | 0.98 | 0.98 |\n| vein endothelial cell | 213 | 0.84 | 0.84 | 0.89 | 0.82 | 0.00 | 0.84 | 0.85 | 0.85 | 0.88 |\n| plasma cell | 138 | 1.00 | 0.99 | 0.99 | 0.99 | 0.00 | 1.00 | 1.00 | 1.00 | 0.99 |\n| endothelial cell of artery | 85 | 0.84 | 0.93 | 0.92 | 0.80 | 0.00 | 0.88 | 0.91 | 0.91 | 0.94 |\n| macrophage | 87 | 0.97 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| CD8-positive, alpha-beta thymocyte | 74 | 0.62 | 0.71 | 0.79 | 0.46 | 0.00 | 0.76 | 0.62 | 0.74 | 0.80 |\n| thymocyte | 48 | 0.52 | 0.60 | 0.78 | 0.41 | 0.00 | 0.76 | 0.61 | 0.75 | 0.81 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 38 | 0.30 | 0.47 | 0.49 | 0.13 | 0.00 | 0.38 | 0.50 | 0.56 | 0.58 |\n| natural killer cell | 44 | 0.97 | 0.98 | 0.97 | 0.89 | 0.00 | 0.97 | 0.96 | 0.93 | 0.97 |\n| endothelial cell of lymphatic vessel | 35 | 1.00 | 1.00 | 1.00 | 0.94 | 0.00 | 0.96 | 0.99 | 0.99 | 1.00 |\n| fibroblast | 22 | 0.53 | 0.16 | 0.21 | 0.65 | 0.00 | 0.88 | 0.75 | 0.86 | 0.93 |\n| vascular associated smooth muscle cell | 15 | 0.74 | 0.00 | 0.57 | 0.58 | 0.00 | 0.82 | 0.97 | 0.87 | 0.77 |\n| mesothelial cell | 15 | 0.93 | 0.89 | 0.97 | 0.90 | 0.00 | 0.87 | 0.93 | 0.90 | 0.97 |\n| erythrocyte | 17 | 0.91 | 0.94 | 0.91 | 0.97 | 0.00 | 0.94 | 0.97 | 0.97 | 0.94 |\n| neuro-medullary thymic epithelial cell | 15 | 0.97 | 0.97 | 0.93 | 0.90 | 0.00 | 0.87 | 1.00 | 0.97 | 1.00 |\n| neutrophil | 12 | 0.74 | 0.92 | 0.92 | 0.83 | 0.00 | 0.88 | 0.92 | 0.87 | 0.88 |\n| hematopoietic precursor cell | 10 | 0.80 | 0.46 | 0.95 | 0.80 | 0.00 | 0.70 | 0.89 | 0.86 | 0.84 |\n| myo-medullary thymic epithelial cell | 5 | 0.91 | 0.75 | 1.00 | 0.80 | 0.00 | 0.91 | 0.91 | 1.00 | 0.91 |\n| medullary thymic epithelial cell | 7 | 1.00 | 0.67 | 0.55 | 0.67 | 0.00 | 0.92 | 0.92 | 1.00 | 0.92 |\n| monocyte | 1 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 0.00 |\n| mast cell | 3 | 0.00 | 0.80 | 0.80 | 0.80 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |\n| fast muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| T follicular helper cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| endothelial 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| CD4-positive, alpha-beta T cell | 6381 | 0.76 | 0.81 | 0.89 | 0.81 | 0.00 | 0.73 | 0.75 | 0.78 | 0.86 |\n| CD4-positive, alpha-beta thymocyte | 4139 | 0.69 | 0.45 | 0.84 | 0.77 | 0.00 | 0.73 | 0.70 | 0.75 | 0.81 |\n| B cell | 4009 | 1.00 | 0.99 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| thymic fibroblast type 2 | 3824 | 0.88 | 0.90 | 0.94 | 0.93 | 0.00 | 0.93 | 0.92 | 0.92 | 0.94 |\n| thymic fibroblast type 1 | 2933 | 0.86 | 0.86 | 0.93 | 0.91 | 0.00 | 0.91 | 0.90 | 0.90 | 0.93 |\n| CD8-positive, alpha-beta T cell | 2527 | 0.79 | 0.83 | 0.90 | 0.85 | 0.00 | 0.83 | 0.82 | 0.84 | 0.87 |\n| capillary endothelial cell | 2346 | 0.82 | 0.85 | 0.94 | 0.89 | 0.00 | 0.89 | 0.89 | 0.88 | 0.92 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 2262 | 0.49 | 0.41 | 0.66 | 0.55 | 0.00 | 0.57 | 0.51 | 0.58 | 0.65 |\n| smooth muscle cell | 2002 | 0.96 | 0.94 | 0.99 | 0.98 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| vein endothelial cell | 1835 | 0.82 | 0.82 | 0.93 | 0.88 | 0.00 | 0.88 | 0.89 | 0.88 | 0.91 |\n| plasma cell | 1440 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of artery | 688 | 0.89 | 0.92 | 0.96 | 0.88 | 0.00 | 0.93 | 0.96 | 0.94 | 0.97 |\n| macrophage | 683 | 0.97 | 0.98 | 0.99 | 0.97 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| CD8-positive, alpha-beta thymocyte | 598 | 0.59 | 0.69 | 0.84 | 0.64 | 0.00 | 0.77 | 0.75 | 0.81 | 0.84 |\n| thymocyte | 407 | 0.57 | 0.62 | 0.83 | 0.47 | 0.00 | 0.86 | 0.79 | 0.87 | 0.91 |\n| naive thymus-derived CD8-positive, alpha-beta T cell | 396 | 0.36 | 0.43 | 0.71 | 0.21 | 0.00 | 0.57 | 0.67 | 0.75 | 0.78 |\n| natural killer cell | 384 | 0.91 | 0.91 | 0.94 | 0.86 | 0.00 | 0.94 | 0.97 | 0.96 | 0.97 |\n| endothelial cell of lymphatic vessel | 336 | 0.97 | 0.97 | 0.98 | 0.93 | 0.00 | 0.94 | 0.99 | 0.98 | 0.99 |\n| fibroblast | 250 | 0.66 | 0.06 | 0.95 | 0.85 | 0.00 | 0.97 | 0.89 | 0.93 | 0.97 |\n| vascular associated smooth muscle cell | 226 | 0.69 | 0.04 | 0.96 | 0.84 | 0.00 | 0.93 | 0.97 | 0.95 | 0.98 |\n| mesothelial cell | 160 | 0.94 | 0.84 | 0.95 | 0.93 | 0.00 | 0.97 | 0.98 | 0.98 | 0.97 |\n| erythrocyte | 135 | 0.95 | 0.92 | 0.92 | 0.96 | 0.00 | 0.93 | 0.99 | 0.94 | 0.97 |\n| neuro-medullary thymic epithelial cell | 120 | 0.92 | 0.92 | 0.90 | 0.91 | 0.00 | 0.90 | 1.00 | 0.99 | 0.98 |\n| neutrophil | 109 | 0.61 | 0.78 | 0.90 | 0.86 | 0.00 | 0.96 | 1.00 | 1.00 | 1.00 |\n| hematopoietic precursor cell | 82 | 0.74 | 0.11 | 0.88 | 0.91 | 0.00 | 0.98 | 1.00 | 0.98 | 1.00 |\n| myo-medullary thymic epithelial cell | 72 | 0.81 | 0.85 | 0.96 | 0.94 | 0.00 | 0.98 | 0.99 | 1.00 | 0.98 |\n| medullary thymic epithelial cell | 36 | 0.86 | 0.52 | 0.87 | 0.76 | 0.00 | 0.99 | 1.00 | 1.00 | 0.96 |\n| monocyte | 25 | 0.00 | 0.00 | 0.82 | 0.62 | 0.00 | 0.86 | 0.98 | 0.96 | 1.00 |\n| mast cell | 21 | 0.00 | 0.84 | 0.89 | 0.85 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| fast muscle cell | 21 | 0.54 | 0.15 | 0.95 | 0.86 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |\n| T follicular helper cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.43 | 0.86 | 0.86 | 0.91 |\n| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.57 | 1.00 | 1.00 |\n| endothelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.22 | 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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         "ENSG00000065600",
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         "ENSG00000104432",
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         "ENSG00000112175",
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         "ENSG00000113924",
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         "ENSG00000125384",
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         "ENSG00000127329",
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