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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| B cell | 5491 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 3913 | 0.79 | 0.87 | 0.86 | 0.85 | 0.00 | 0.63 | 0.63 | 0.78 | 0.87 |\n| CD8-positive, alpha-beta T cell | 1463 | 0.79 | 0.81 | 0.80 | 0.75 | 0.00 | 0.70 | 0.75 | 0.85 | 0.83 |\n| plasma cell | 601 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 413 | 0.15 | 0.02 | 0.04 | 0.07 | 0.00 | 0.33 | 0.38 | 0.54 | 0.23 |\n| macrophage | 165 | 0.92 | 0.91 | 0.91 | 0.90 | 0.00 | 0.87 | 0.87 | 0.90 | 0.92 |\n| natural killer cell | 182 | 0.65 | 0.73 | 0.69 | 0.62 | 0.00 | 0.60 | 0.55 | 0.66 | 0.67 |\n| T cell | 122 | 0.62 | 0.73 | 0.67 | 0.64 | 0.00 | 0.45 | 0.45 | 0.60 | 0.69 |\n| mature NK T cell | 119 | 0.50 | 0.48 | 0.51 | 0.44 | 0.00 | 0.46 | 0.44 | 0.55 | 0.53 |\n| regulatory T cell | 97 | 0.25 | 0.02 | 0.21 | 0.10 | 0.00 | 0.21 | 0.19 | 0.24 | 0.34 |\n| monocyte | 67 | 0.79 | 0.79 | 0.75 | 0.73 | 0.00 | 0.65 | 0.78 | 0.86 | 0.86 |\n| innate lymphoid cell | 86 | 0.64 | 0.66 | 0.51 | 0.39 | 0.00 | 0.54 | 0.53 | 0.62 | 0.68 |\n| classical monocyte | 52 | 0.72 | 0.73 | 0.65 | 0.53 | 0.00 | 0.67 | 0.68 | 0.82 | 0.76 |\n| neutrophil | 25 | 1.00 | 0.98 | 0.98 | 0.91 | 0.00 | 0.67 | 0.96 | 0.96 | 0.96 |\n| intermediate monocyte | 22 | 0.52 | 0.47 | 0.38 | 0.22 | 0.00 | 0.55 | 0.65 | 0.88 | 0.68 |\n| mast cell | 18 | 1.00 | 1.00 | 0.94 | 1.00 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |\n| endothelial cell | 22 | 0.71 | 0.61 | 0.67 | 0.56 | 0.00 | 0.76 | 0.81 | 0.83 | 0.77 |\n| myeloid dendritic cell | 13 | 0.60 | 0.54 | 0.52 | 0.12 | 0.00 | 0.26 | 0.67 | 0.65 | 0.71 |\n| CD4-positive, alpha-beta thymocyte | 9 | 0.00 | 0.00 | 0.00 | 0.18 | 0.00 | 0.22 | 0.10 | 0.21 | 0.20 |\n| stromal cell | 12 | 0.83 | 0.87 | 0.74 | 0.81 | 0.00 | 0.92 | 0.92 | 0.96 | 0.92 |\n| non-classical monocyte | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.13 | 0.71 | 0.22 |\n| CD8-positive, alpha-beta thymocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.29 | 0.57 | 0.00 |\n| erythrocyte | 2 | 0.40 | 0.50 | 0.44 | 0.50 | 0.00 | 0.57 | 1.00 | 1.00 | 1.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| hematopoietic precursor cell | 3 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 | 0.31 | 0.00 | 0.50 | 0.00 |",
-    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 49255 | 0.99 | 1.00 | 1.00 | 1.00 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 35367 | 0.79 | 0.88 | 0.89 | 0.88 | 0.00 | 0.61 | 0.64 | 0.78 | 0.88 |\n| CD8-positive, alpha-beta T cell | 13219 | 0.79 | 0.82 | 0.86 | 0.81 | 0.00 | 0.71 | 0.78 | 0.86 | 0.86 |\n| plasma cell | 5343 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 3741 | 0.18 | 0.02 | 0.18 | 0.18 | 0.00 | 0.33 | 0.40 | 0.55 | 0.32 |\n| macrophage | 1629 | 0.90 | 0.92 | 0.93 | 0.92 | 0.00 | 0.90 | 0.93 | 0.94 | 0.94 |\n| natural killer cell | 1397 | 0.65 | 0.72 | 0.78 | 0.75 | 0.00 | 0.71 | 0.70 | 0.76 | 0.81 |\n| T cell | 1159 | 0.61 | 0.73 | 0.76 | 0.73 | 0.00 | 0.45 | 0.48 | 0.65 | 0.71 |\n| mature NK T cell | 905 | 0.50 | 0.44 | 0.63 | 0.61 | 0.00 | 0.60 | 0.60 | 0.68 | 0.74 |\n| regulatory T cell | 871 | 0.23 | 0.02 | 0.40 | 0.22 | 0.00 | 0.24 | 0.23 | 0.25 | 0.40 |\n| monocyte | 699 | 0.80 | 0.79 | 0.84 | 0.87 | 0.00 | 0.73 | 0.83 | 0.90 | 0.95 |\n| innate lymphoid cell | 659 | 0.57 | 0.65 | 0.60 | 0.60 | 0.00 | 0.73 | 0.57 | 0.66 | 0.73 |\n| classical monocyte | 500 | 0.64 | 0.67 | 0.74 | 0.68 | 0.00 | 0.80 | 0.88 | 0.90 | 0.87 |\n| neutrophil | 278 | 0.98 | 0.97 | 0.99 | 0.95 | 0.00 | 0.82 | 0.99 | 0.96 | 0.97 |\n| intermediate monocyte | 259 | 0.48 | 0.49 | 0.63 | 0.56 | 0.00 | 0.77 | 0.89 | 0.91 | 0.85 |\n| mast cell | 194 | 0.97 | 0.97 | 0.97 | 0.96 | 0.00 | 0.91 | 0.98 | 0.98 | 0.97 |\n| endothelial cell | 174 | 0.68 | 0.65 | 0.77 | 0.78 | 0.00 | 0.85 | 0.93 | 0.94 | 0.91 |\n| myeloid dendritic cell | 109 | 0.50 | 0.54 | 0.60 | 0.55 | 0.00 | 0.22 | 0.91 | 0.91 | 0.87 |\n| CD4-positive, alpha-beta thymocyte | 113 | 0.00 | 0.00 | 0.03 | 0.20 | 0.00 | 0.39 | 0.50 | 0.76 | 0.55 |\n| stromal cell | 99 | 0.84 | 0.45 | 0.82 | 0.88 | 0.00 | 0.88 | 0.98 | 0.99 | 0.97 |\n| non-classical monocyte | 65 | 0.00 | 0.09 | 0.26 | 0.09 | 0.00 | 0.63 | 0.82 | 0.79 | 0.75 |\n| CD8-positive, alpha-beta thymocyte | 56 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.32 | 0.68 | 0.75 | 0.60 |\n| erythrocyte | 40 | 0.84 | 0.79 | 0.69 | 0.85 | 0.00 | 0.73 | 0.96 | 0.86 | 0.93 |\n| plasmacytoid dendritic cell | 15 | 0.00 | 0.64 | 0.81 | 0.74 | 0.00 | 0.27 | 1.00 | 1.00 | 1.00 |\n| hematopoietic precursor cell | 9 | 0.00 | 0.00 | 0.53 | 0.35 | 0.00 | 0.33 | 0.95 | 0.90 | 0.75 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| B cell | 5485 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 3937 | 0.76 | 0.88 | 0.86 | 0.85 | 0.00 | 0.56 | 0.63 | 0.78 | 0.86 |\n| CD8-positive, alpha-beta T cell | 1453 | 0.79 | 0.81 | 0.80 | 0.75 | 0.00 | 0.73 | 0.76 | 0.84 | 0.84 |\n| plasma cell | 604 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 415 | 0.21 | 0.04 | 0.05 | 0.06 | 0.00 | 0.28 | 0.38 | 0.55 | 0.32 |\n| macrophage | 162 | 0.91 | 0.91 | 0.89 | 0.88 | 0.00 | 0.85 | 0.86 | 0.89 | 0.92 |\n| natural killer cell | 176 | 0.62 | 0.73 | 0.68 | 0.63 | 0.00 | 0.67 | 0.54 | 0.64 | 0.71 |\n| T cell | 121 | 0.62 | 0.76 | 0.68 | 0.64 | 0.00 | 0.57 | 0.47 | 0.63 | 0.67 |\n| mature NK T cell | 116 | 0.48 | 0.46 | 0.50 | 0.47 | 0.00 | 0.48 | 0.48 | 0.55 | 0.58 |\n| regulatory T cell | 93 | 0.23 | 0.00 | 0.09 | 0.07 | 0.00 | 0.15 | 0.19 | 0.23 | 0.34 |\n| monocyte | 69 | 0.78 | 0.83 | 0.76 | 0.74 | 0.00 | 0.74 | 0.78 | 0.83 | 0.88 |\n| innate lymphoid cell | 85 | 0.61 | 0.65 | 0.48 | 0.40 | 0.00 | 0.49 | 0.55 | 0.64 | 0.65 |\n| classical monocyte | 52 | 0.69 | 0.74 | 0.66 | 0.59 | 0.00 | 0.74 | 0.68 | 0.81 | 0.78 |\n| neutrophil | 27 | 0.87 | 0.96 | 0.98 | 1.00 | 0.00 | 0.95 | 0.94 | 0.89 | 0.95 |\n| intermediate monocyte | 22 | 0.47 | 0.51 | 0.38 | 0.30 | 0.00 | 0.47 | 0.67 | 0.83 | 0.70 |\n| mast cell | 17 | 1.00 | 1.00 | 0.97 | 0.97 | 0.00 | 0.92 | 1.00 | 1.00 | 1.00 |\n| endothelial cell | 24 | 0.74 | 0.80 | 0.72 | 0.67 | 0.00 | 0.73 | 0.84 | 0.71 | 0.81 |\n| myeloid dendritic cell | 13 | 0.59 | 0.64 | 0.55 | 0.11 | 0.00 | 0.34 | 0.55 | 0.73 | 0.69 |\n| CD4-positive, alpha-beta thymocyte | 9 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.21 | 0.16 | 0.24 | 0.00 |\n| stromal cell | 12 | 0.80 | 0.70 | 0.74 | 0.64 | 0.00 | 0.75 | 0.88 | 0.88 | 0.89 |\n| non-classical monocyte | 6 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 | 0.07 | 0.31 | 0.92 | 0.25 |\n| CD8-positive, alpha-beta thymocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.44 | 0.36 | 0.00 |\n| erythrocyte | 2 | 0.40 | 0.50 | 0.29 | 0.67 | 0.00 | 0.36 | 0.80 | 1.00 | 1.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 |\n| hematopoietic precursor cell | 3 | 0.00 | 0.00 | 0.50 | 0.40 | 0.00 | 0.22 | 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| B cell | 49261 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 35343 | 0.74 | 0.88 | 0.89 | 0.88 | 0.00 | 0.59 | 0.63 | 0.79 | 0.87 |\n| CD8-positive, alpha-beta T cell | 13229 | 0.78 | 0.82 | 0.86 | 0.81 | 0.00 | 0.75 | 0.78 | 0.86 | 0.85 |\n| plasma cell | 5340 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 3739 | 0.21 | 0.01 | 0.18 | 0.16 | 0.00 | 0.29 | 0.39 | 0.56 | 0.35 |\n| macrophage | 1632 | 0.91 | 0.92 | 0.93 | 0.92 | 0.00 | 0.89 | 0.93 | 0.95 | 0.94 |\n| natural killer cell | 1403 | 0.63 | 0.72 | 0.79 | 0.75 | 0.00 | 0.73 | 0.71 | 0.75 | 0.81 |\n| T cell | 1160 | 0.62 | 0.72 | 0.77 | 0.73 | 0.00 | 0.59 | 0.48 | 0.67 | 0.69 |\n| mature NK T cell | 908 | 0.50 | 0.44 | 0.64 | 0.63 | 0.00 | 0.59 | 0.60 | 0.68 | 0.73 |\n| regulatory T cell | 875 | 0.22 | 0.01 | 0.39 | 0.25 | 0.00 | 0.19 | 0.23 | 0.26 | 0.39 |\n| monocyte | 697 | 0.78 | 0.79 | 0.84 | 0.84 | 0.00 | 0.83 | 0.87 | 0.92 | 0.93 |\n| innate lymphoid cell | 660 | 0.57 | 0.64 | 0.58 | 0.55 | 0.00 | 0.70 | 0.59 | 0.67 | 0.73 |\n| classical monocyte | 500 | 0.58 | 0.67 | 0.72 | 0.69 | 0.00 | 0.82 | 0.86 | 0.91 | 0.86 |\n| neutrophil | 276 | 0.86 | 0.96 | 0.99 | 0.96 | 0.00 | 0.96 | 1.00 | 0.97 | 0.97 |\n| intermediate monocyte | 259 | 0.50 | 0.51 | 0.63 | 0.57 | 0.00 | 0.77 | 0.89 | 0.93 | 0.85 |\n| mast cell | 195 | 0.97 | 0.97 | 0.96 | 0.96 | 0.00 | 0.92 | 0.98 | 0.98 | 0.97 |\n| endothelial cell | 172 | 0.67 | 0.65 | 0.74 | 0.72 | 0.00 | 0.73 | 0.96 | 0.93 | 0.88 |\n| myeloid dendritic cell | 109 | 0.50 | 0.52 | 0.62 | 0.50 | 0.00 | 0.29 | 0.90 | 0.95 | 0.87 |\n| CD4-positive, alpha-beta thymocyte | 113 | 0.00 | 0.00 | 0.08 | 0.20 | 0.00 | 0.42 | 0.47 | 0.78 | 0.55 |\n| stromal cell | 99 | 0.84 | 0.51 | 0.85 | 0.77 | 0.00 | 0.71 | 0.98 | 0.97 | 0.95 |\n| non-classical monocyte | 65 | 0.00 | 0.06 | 0.26 | 0.14 | 0.00 | 0.39 | 0.74 | 0.84 | 0.57 |\n| CD8-positive, alpha-beta thymocyte | 56 | 0.00 | 0.00 | 0.04 | 0.07 | 0.00 | 0.29 | 0.74 | 0.65 | 0.63 |\n| erythrocyte | 40 | 0.82 | 0.82 | 0.67 | 0.84 | 0.00 | 0.51 | 0.92 | 0.93 | 0.95 |\n| plasmacytoid dendritic cell | 15 | 0.00 | 0.70 | 0.81 | 0.81 | 0.00 | 0.23 | 0.97 | 0.97 | 0.97 |\n| hematopoietic precursor cell | 9 | 0.00 | 0.00 | 0.59 | 0.38 | 0.00 | 0.44 | 0.95 | 0.95 | 0.89 |"
 }

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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         "ENSG00000008300",
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