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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| neutrophil | 882 | 0.97 | 0.97 | 0.97 | 0.96 | 0.00 | 0.93 | 0.95 | 0.95 | 0.98 |\n| CD4-positive, alpha-beta T cell | 298 | 0.84 | 0.84 | 0.84 | 0.83 | 0.00 | 0.81 | 0.86 | 0.90 | 0.88 |\n| CD8-positive, alpha-beta T cell | 257 | 0.82 | 0.82 | 0.82 | 0.80 | 0.00 | 0.80 | 0.85 | 0.87 | 0.86 |\n| monocyte | 234 | 0.77 | 0.79 | 0.81 | 0.79 | 0.00 | 0.64 | 0.71 | 0.79 | 0.82 |\n| B cell | 191 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| hematopoietic precursor cell | 165 | 0.76 | 0.82 | 0.85 | 0.80 | 0.00 | 0.78 | 0.83 | 0.86 | 0.86 |\n| plasma cell | 143 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 1.00 | 0.99 |\n| natural killer cell | 107 | 0.92 | 0.94 | 0.96 | 0.90 | 0.00 | 0.89 | 0.96 | 0.96 | 0.96 |\n| erythroid progenitor cell | 93 | 0.74 | 0.74 | 0.68 | 0.69 | 0.00 | 0.74 | 0.83 | 0.84 | 0.80 |\n| hematopoietic stem cell | 79 | 0.73 | 0.81 | 0.82 | 0.79 | 0.00 | 0.76 | 0.82 | 0.89 | 0.85 |\n| granulocyte | 62 | 0.67 | 0.33 | 0.63 | 0.35 | 0.00 | 0.47 | 0.68 | 0.60 | 0.77 |\n| erythrocyte | 45 | 0.58 | 0.61 | 0.67 | 0.58 | 0.00 | 0.68 | 0.85 | 0.78 | 0.76 |\n| common myeloid progenitor | 48 | 0.65 | 0.75 | 0.64 | 0.62 | 0.00 | 0.73 | 0.75 | 0.84 | 0.77 |\n| macrophage | 33 | 0.67 | 0.48 | 0.73 | 0.55 | 0.00 | 0.54 | 0.61 | 0.72 | 0.72 |\n| classical monocyte | 18 | 0.00 | 0.00 | 0.12 | 0.06 | 0.00 | 0.22 | 0.21 | 0.38 | 0.15 |\n| intermediate monocyte | 21 | 0.47 | 0.39 | 0.41 | 0.29 | 0.00 | 0.29 | 0.36 | 0.36 | 0.48 |\n| myeloid dendritic cell | 6 | 0.40 | 0.20 | 0.40 | 0.53 | 0.00 | 0.33 | 0.33 | 0.71 | 0.62 |\n| T cell | 13 | 0.55 | 0.27 | 0.48 | 0.20 | 0.00 | 0.39 | 0.76 | 0.73 | 0.80 |\n| mature NK T cell | 8 | 0.00 | 0.40 | 0.40 | 0.20 | 0.00 | 0.33 | 0.36 | 0.40 | 0.40 |\n| non-classical monocyte | 7 | 0.00 | 0.44 | 0.00 | 0.25 | 0.00 | 0.31 | 0.20 | 0.46 | 0.25 |\n| basophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| regulatory T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| fibroblast | 1 | 0.00 | 1.00 | 1.00 | 0.50 | 0.00 | 0.50 | 0.00 | 0.00 | 1.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.40 | 0.00 | 1.00 | 1.00 |\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| neutrophil | 7795 | 0.97 | 0.96 | 0.98 | 0.97 | 0.00 | 0.96 | 0.96 | 0.95 | 0.98 |\n| CD4-positive, alpha-beta T cell | 2875 | 0.86 | 0.86 | 0.90 | 0.87 | 0.00 | 0.84 | 0.90 | 0.92 | 0.90 |\n| CD8-positive, alpha-beta T cell | 2379 | 0.83 | 0.84 | 0.88 | 0.83 | 0.00 | 0.83 | 0.87 | 0.89 | 0.88 |\n| monocyte | 1806 | 0.77 | 0.80 | 0.87 | 0.85 | 0.00 | 0.73 | 0.82 | 0.86 | 0.90 |\n| B cell | 1628 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| hematopoietic precursor cell | 1555 | 0.80 | 0.85 | 0.92 | 0.89 | 0.00 | 0.86 | 0.90 | 0.91 | 0.93 |\n| plasma cell | 1305 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| natural killer cell | 992 | 0.93 | 0.94 | 0.96 | 0.90 | 0.00 | 0.93 | 0.96 | 0.96 | 0.97 |\n| erythroid progenitor cell | 878 | 0.71 | 0.74 | 0.83 | 0.84 | 0.00 | 0.88 | 0.93 | 0.95 | 0.94 |\n| hematopoietic stem cell | 713 | 0.75 | 0.83 | 0.89 | 0.87 | 0.00 | 0.83 | 0.94 | 0.96 | 0.93 |\n| granulocyte | 573 | 0.72 | 0.25 | 0.76 | 0.60 | 0.00 | 0.67 | 0.70 | 0.70 | 0.84 |\n| erythrocyte | 408 | 0.62 | 0.66 | 0.80 | 0.81 | 0.00 | 0.89 | 0.95 | 0.95 | 0.94 |\n| common myeloid progenitor | 405 | 0.64 | 0.66 | 0.76 | 0.78 | 0.00 | 0.78 | 0.92 | 0.95 | 0.91 |\n| macrophage | 325 | 0.58 | 0.54 | 0.75 | 0.73 | 0.00 | 0.83 | 0.91 | 0.92 | 0.93 |\n| classical monocyte | 213 | 0.00 | 0.01 | 0.41 | 0.39 | 0.00 | 0.46 | 0.76 | 0.80 | 0.75 |\n| intermediate monocyte | 203 | 0.41 | 0.48 | 0.69 | 0.60 | 0.00 | 0.71 | 0.89 | 0.92 | 0.85 |\n| myeloid dendritic cell | 102 | 0.57 | 0.50 | 0.70 | 0.72 | 0.00 | 0.74 | 0.75 | 0.81 | 0.82 |\n| T cell | 85 | 0.43 | 0.10 | 0.39 | 0.38 | 0.00 | 0.45 | 0.72 | 0.72 | 0.75 |\n| mature NK T cell | 56 | 0.00 | 0.39 | 0.51 | 0.15 | 0.00 | 0.53 | 0.94 | 0.90 | 0.95 |\n| non-classical monocyte | 46 | 0.00 | 0.18 | 0.54 | 0.38 | 0.00 | 0.80 | 0.98 | 0.95 | 0.85 |\n| basophil | 23 | 0.00 | 0.08 | 0.54 | 0.61 | 0.00 | 0.41 | 0.85 | 0.77 | 0.78 |\n| regulatory T cell | 14 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.37 | 0.88 | 0.82 | 0.12 |\n| fibroblast | 10 | 0.00 | 0.48 | 0.67 | 0.40 | 0.00 | 0.32 | 0.87 | 0.87 | 0.82 |\n| plasmacytoid dendritic cell | 8 | 0.00 | 0.52 | 0.53 | 0.47 | 0.00 | 0.29 | 0.80 | 0.73 | 0.70 |\n| endothelial cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.86 | 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| neutrophil | 887 | 0.97 | 0.96 | 0.97 | 0.96 | 0.00 | 0.92 | 0.95 | 0.95 | 0.98 |\n| CD4-positive, alpha-beta T cell | 302 | 0.84 | 0.86 | 0.84 | 0.81 | 0.00 | 0.83 | 0.86 | 0.89 | 0.87 |\n| CD8-positive, alpha-beta T cell | 251 | 0.81 | 0.84 | 0.82 | 0.75 | 0.00 | 0.78 | 0.83 | 0.87 | 0.85 |\n| monocyte | 233 | 0.77 | 0.80 | 0.81 | 0.77 | 0.00 | 0.67 | 0.67 | 0.75 | 0.80 |\n| B cell | 195 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| hematopoietic precursor cell | 173 | 0.80 | 0.83 | 0.84 | 0.83 | 0.00 | 0.79 | 0.81 | 0.84 | 0.86 |\n| plasma cell | 132 | 0.99 | 1.00 | 0.99 | 1.00 | 0.00 | 0.98 | 1.00 | 0.99 | 1.00 |\n| natural killer cell | 94 | 0.91 | 0.95 | 0.94 | 0.89 | 0.00 | 0.86 | 0.94 | 0.93 | 0.96 |\n| erythroid progenitor cell | 97 | 0.70 | 0.75 | 0.71 | 0.71 | 0.00 | 0.72 | 0.80 | 0.82 | 0.79 |\n| hematopoietic stem cell | 78 | 0.75 | 0.82 | 0.86 | 0.82 | 0.00 | 0.86 | 0.80 | 0.84 | 0.85 |\n| granulocyte | 64 | 0.69 | 0.34 | 0.69 | 0.37 | 0.00 | 0.48 | 0.64 | 0.63 | 0.80 |\n| erythrocyte | 43 | 0.66 | 0.64 | 0.67 | 0.66 | 0.00 | 0.62 | 0.80 | 0.75 | 0.70 |\n| common myeloid progenitor | 47 | 0.64 | 0.75 | 0.64 | 0.67 | 0.00 | 0.69 | 0.69 | 0.85 | 0.73 |\n| macrophage | 38 | 0.56 | 0.47 | 0.64 | 0.59 | 0.00 | 0.63 | 0.66 | 0.69 | 0.72 |\n| classical monocyte | 22 | 0.08 | 0.00 | 0.15 | 0.11 | 0.00 | 0.25 | 0.14 | 0.26 | 0.07 |\n| intermediate monocyte | 21 | 0.45 | 0.49 | 0.53 | 0.32 | 0.00 | 0.37 | 0.41 | 0.47 | 0.52 |\n| myeloid dendritic cell | 7 | 0.36 | 0.33 | 0.62 | 0.46 | 0.00 | 0.46 | 0.44 | 0.67 | 0.58 |\n| T cell | 12 | 0.52 | 0.15 | 0.38 | 0.27 | 0.00 | 0.42 | 0.55 | 0.67 | 0.76 |\n| mature NK T cell | 7 | 0.00 | 0.44 | 0.00 | 0.00 | 0.00 | 0.33 | 0.55 | 0.22 | 0.40 |\n| non-classical monocyte | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 0.22 | 0.43 | 0.00 |\n| basophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| regulatory T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| fibroblast | 1 | 0.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.25 | 0.00 | 0.00 | 1.00 |\n| plasmacytoid dendritic cell | 2 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.67 | 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| neutrophil | 7790 | 0.97 | 0.96 | 0.98 | 0.97 | 0.00 | 0.96 | 0.96 | 0.95 | 0.98 |\n| CD4-positive, alpha-beta T cell | 2871 | 0.85 | 0.86 | 0.90 | 0.86 | 0.00 | 0.86 | 0.88 | 0.92 | 0.90 |\n| CD8-positive, alpha-beta T cell | 2385 | 0.82 | 0.84 | 0.89 | 0.81 | 0.00 | 0.82 | 0.86 | 0.89 | 0.88 |\n| monocyte | 1807 | 0.79 | 0.80 | 0.86 | 0.84 | 0.00 | 0.76 | 0.81 | 0.86 | 0.89 |\n| B cell | 1624 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| hematopoietic precursor cell | 1547 | 0.81 | 0.86 | 0.92 | 0.89 | 0.00 | 0.85 | 0.88 | 0.89 | 0.93 |\n| plasma cell | 1316 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| natural killer cell | 1005 | 0.92 | 0.94 | 0.96 | 0.88 | 0.00 | 0.91 | 0.96 | 0.95 | 0.97 |\n| erythroid progenitor cell | 874 | 0.71 | 0.74 | 0.82 | 0.83 | 0.00 | 0.90 | 0.93 | 0.96 | 0.94 |\n| hematopoietic stem cell | 714 | 0.74 | 0.83 | 0.89 | 0.87 | 0.00 | 0.88 | 0.93 | 0.94 | 0.94 |\n| granulocyte | 571 | 0.70 | 0.25 | 0.78 | 0.46 | 0.00 | 0.72 | 0.73 | 0.70 | 0.84 |\n| erythrocyte | 410 | 0.70 | 0.66 | 0.80 | 0.79 | 0.00 | 0.90 | 0.96 | 0.96 | 0.92 |\n| common myeloid progenitor | 406 | 0.62 | 0.65 | 0.76 | 0.77 | 0.00 | 0.82 | 0.91 | 0.95 | 0.91 |\n| macrophage | 320 | 0.60 | 0.57 | 0.72 | 0.69 | 0.00 | 0.82 | 0.91 | 0.93 | 0.92 |\n| classical monocyte | 209 | 0.08 | 0.00 | 0.38 | 0.39 | 0.00 | 0.55 | 0.69 | 0.77 | 0.73 |\n| intermediate monocyte | 203 | 0.42 | 0.48 | 0.66 | 0.53 | 0.00 | 0.71 | 0.88 | 0.92 | 0.85 |\n| myeloid dendritic cell | 101 | 0.50 | 0.47 | 0.72 | 0.72 | 0.00 | 0.69 | 0.81 | 0.83 | 0.89 |\n| T cell | 86 | 0.40 | 0.16 | 0.44 | 0.38 | 0.00 | 0.44 | 0.66 | 0.63 | 0.67 |\n| mature NK T cell | 57 | 0.00 | 0.47 | 0.54 | 0.13 | 0.00 | 0.69 | 0.95 | 0.94 | 0.97 |\n| non-classical monocyte | 47 | 0.00 | 0.25 | 0.48 | 0.33 | 0.00 | 0.81 | 0.93 | 0.97 | 0.86 |\n| basophil | 23 | 0.00 | 0.00 | 0.64 | 0.63 | 0.00 | 0.55 | 0.82 | 0.75 | 0.81 |\n| regulatory T cell | 14 | 0.00 | 0.00 | 0.22 | 0.00 | 0.00 | 0.61 | 0.85 | 0.70 | 0.24 |\n| fibroblast | 10 | 0.00 | 0.55 | 0.61 | 0.61 | 0.00 | 0.30 | 0.91 | 0.95 | 0.91 |\n| plasmacytoid dendritic cell | 7 | 0.00 | 0.12 | 0.46 | 0.62 | 0.00 | 0.40 | 0.93 | 0.88 | 0.88 |\n| endothelial cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.60 | 1.00 | 1.00 | 0.50 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

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         "ENSG00000005187",
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