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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 | 407 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| macrophage | 335 | 0.96 | 0.97 | 0.96 | 0.96 | 0.00 | 0.94 | 0.96 | 0.96 | 0.98 |\n| T cell | 261 | 0.73 | 0.77 | 0.72 | 0.66 | 0.00 | 0.70 | 0.67 | 0.82 | 0.82 |\n| endothelial cell | 200 | 0.99 | 0.98 | 0.98 | 0.98 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| mast cell | 220 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| CD8-positive, alpha-beta T cell | 129 | 0.66 | 0.71 | 0.62 | 0.38 | 0.00 | 0.68 | 0.82 | 0.90 | 0.76 |\n| smooth muscle cell | 55 | 0.86 | 0.91 | 0.88 | 0.88 | 0.00 | 0.87 | 0.86 | 0.85 | 0.87 |\n| CD4-positive, alpha-beta T cell | 34 | 0.27 | 0.08 | 0.14 | 0.10 | 0.00 | 0.25 | 0.25 | 0.29 | 0.36 |\n| neutrophil | 29 | 0.95 | 0.98 | 0.97 | 0.92 | 0.00 | 0.91 | 0.95 | 0.91 | 0.95 |\n| regulatory T cell | 25 | 0.63 | 0.68 | 0.42 | 0.06 | 0.00 | 0.55 | 0.52 | 0.66 | 0.68 |\n| sebum secreting cell | 13 | 0.79 | 0.81 | 0.87 | 0.87 | 0.00 | 0.81 | 0.90 | 0.80 | 0.84 |\n| myeloid dendritic cell | 16 | 0.67 | 0.69 | 0.61 | 0.50 | 0.00 | 0.51 | 0.73 | 0.68 | 0.83 |\n| melanocyte | 14 | 0.81 | 0.81 | 0.86 | 0.81 | 0.00 | 0.79 | 0.79 | 0.67 | 0.81 |\n| plasma cell | 10 | 0.95 | 1.00 | 0.95 | 0.86 | 0.00 | 0.87 | 0.95 | 1.00 | 1.00 |\n| Langerhans cell | 10 | 0.67 | 0.47 | 0.40 | 0.78 | 0.00 | 0.49 | 0.74 | 0.64 | 0.75 |\n| natural killer cell | 3 | 0.50 | 0.00 | 0.00 | 0.50 | 0.00 | 0.25 | 0.40 | 0.40 | 0.57 |\n| mature NK T cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.22 | 0.29 | 0.29 | 0.00 |\n| keratocyte | 2 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.67 | 0.67 |\n| basophil | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 0.00 |\n| epithelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 0.00 | 0.00 |\n| B cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| erythrocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| stromal cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| activated CD4-positive, alpha-beta T 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 | 3722 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| macrophage | 2981 | 0.95 | 0.97 | 0.98 | 0.98 | 0.00 | 0.95 | 0.97 | 0.98 | 0.98 |\n| T cell | 2375 | 0.70 | 0.74 | 0.81 | 0.79 | 0.00 | 0.75 | 0.80 | 0.88 | 0.88 |\n| endothelial cell | 1875 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |\n| mast cell | 1781 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| CD8-positive, alpha-beta T cell | 1402 | 0.69 | 0.70 | 0.77 | 0.63 | 0.00 | 0.76 | 0.89 | 0.94 | 0.87 |\n| smooth muscle cell | 449 | 0.84 | 0.87 | 0.88 | 0.88 | 0.00 | 0.89 | 0.88 | 0.88 | 0.87 |\n| CD4-positive, alpha-beta T cell | 331 | 0.20 | 0.09 | 0.40 | 0.38 | 0.00 | 0.43 | 0.59 | 0.67 | 0.70 |\n| neutrophil | 261 | 0.99 | 1.00 | 0.99 | 0.97 | 0.00 | 0.94 | 0.98 | 0.97 | 0.99 |\n| regulatory T cell | 248 | 0.61 | 0.60 | 0.74 | 0.37 | 0.00 | 0.78 | 0.83 | 0.84 | 0.84 |\n| sebum secreting cell | 122 | 0.83 | 0.89 | 0.91 | 0.89 | 0.00 | 0.87 | 0.97 | 0.98 | 0.93 |\n| myeloid dendritic cell | 92 | 0.45 | 0.37 | 0.63 | 0.71 | 0.00 | 0.65 | 0.70 | 0.81 | 0.74 |\n| melanocyte | 92 | 0.81 | 0.81 | 0.86 | 0.77 | 0.00 | 0.83 | 0.98 | 0.94 | 0.91 |\n| plasma cell | 76 | 0.97 | 0.94 | 1.00 | 0.90 | 0.00 | 0.88 | 0.98 | 0.99 | 0.99 |\n| Langerhans cell | 66 | 0.52 | 0.50 | 0.73 | 0.70 | 0.00 | 0.53 | 0.66 | 0.80 | 0.75 |\n| natural killer cell | 61 | 0.46 | 0.07 | 0.49 | 0.45 | 0.00 | 0.70 | 0.75 | 0.81 | 0.80 |\n| mature NK T cell | 29 | 0.00 | 0.00 | 0.40 | 0.11 | 0.00 | 0.63 | 0.85 | 0.84 | 0.91 |\n| keratocyte | 12 | 0.00 | 0.00 | 0.96 | 0.70 | 0.00 | 0.50 | 1.00 | 0.96 | 1.00 |\n| basophil | 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.19 | 1.00 | 1.00 | 0.00 |\n| epithelial cell | 7 | 0.00 | 0.00 | 0.00 | 0.36 | 0.00 | 0.74 | 0.88 | 1.00 | 0.73 |\n| B cell | 7 | 0.00 | 0.00 | 0.92 | 0.73 | 0.00 | 0.78 | 1.00 | 0.88 | 1.00 |\n| erythrocyte | 5 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 | 0.91 | 1.00 | 1.00 | 1.00 |\n| stromal cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 1.00 | 1.00 | 0.86 |\n| muscle cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.29 | 1.00 | 1.00 | 1.00 |\n| activated CD4-positive, alpha-beta T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| fibroblast | 421 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| macrophage | 325 | 0.96 | 0.97 | 0.96 | 0.95 | 0.00 | 0.92 | 0.96 | 0.96 | 0.97 |\n| T cell | 255 | 0.68 | 0.77 | 0.71 | 0.67 | 0.00 | 0.72 | 0.73 | 0.81 | 0.82 |\n| endothelial cell | 199 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| mast cell | 226 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| CD8-positive, alpha-beta T cell | 133 | 0.67 | 0.72 | 0.66 | 0.50 | 0.00 | 0.75 | 0.83 | 0.90 | 0.82 |\n| smooth muscle cell | 52 | 0.85 | 0.89 | 0.88 | 0.83 | 0.00 | 0.88 | 0.85 | 0.83 | 0.86 |\n| CD4-positive, alpha-beta T cell | 33 | 0.27 | 0.17 | 0.06 | 0.03 | 0.00 | 0.22 | 0.26 | 0.22 | 0.28 |\n| neutrophil | 31 | 0.95 | 0.97 | 0.98 | 0.80 | 0.00 | 0.90 | 0.95 | 0.91 | 0.95 |\n| regulatory T cell | 22 | 0.59 | 0.62 | 0.44 | 0.13 | 0.00 | 0.49 | 0.42 | 0.64 | 0.54 |\n| sebum secreting cell | 13 | 0.75 | 0.83 | 0.83 | 0.83 | 0.00 | 0.92 | 0.92 | 0.85 | 0.86 |\n| myeloid dendritic cell | 16 | 0.73 | 0.60 | 0.51 | 0.57 | 0.00 | 0.54 | 0.74 | 0.72 | 0.81 |\n| melanocyte | 15 | 0.81 | 0.84 | 0.84 | 0.77 | 0.00 | 0.82 | 0.79 | 0.73 | 0.81 |\n| plasma cell | 10 | 0.78 | 0.95 | 0.89 | 0.40 | 0.00 | 0.82 | 0.95 | 0.95 | 0.95 |\n| Langerhans cell | 8 | 0.60 | 0.50 | 0.46 | 0.57 | 0.00 | 0.42 | 0.64 | 0.61 | 0.67 |\n| natural killer cell | 3 | 0.40 | 0.00 | 0.00 | 0.33 | 0.00 | 0.18 | 0.40 | 0.40 | 0.40 |\n| mature NK T cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.00 | 0.00 | 0.00 |\n| keratocyte | 2 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.50 | 1.00 | 0.67 | 1.00 |\n| basophil | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| epithelial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| B cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| erythrocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| stromal cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| activated CD4-positive, alpha-beta T 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 | 3709 | 0.98 | 0.97 | 0.99 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |\n| macrophage | 2992 | 0.96 | 0.96 | 0.98 | 0.97 | 0.00 | 0.94 | 0.97 | 0.98 | 0.98 |\n| T cell | 2381 | 0.68 | 0.75 | 0.81 | 0.78 | 0.00 | 0.79 | 0.80 | 0.88 | 0.87 |\n| endothelial cell | 1875 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |\n| mast cell | 1775 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| CD8-positive, alpha-beta T cell | 1398 | 0.69 | 0.72 | 0.78 | 0.65 | 0.00 | 0.81 | 0.88 | 0.94 | 0.88 |\n| smooth muscle cell | 452 | 0.85 | 0.86 | 0.89 | 0.87 | 0.00 | 0.86 | 0.89 | 0.88 | 0.87 |\n| CD4-positive, alpha-beta T cell | 332 | 0.25 | 0.11 | 0.41 | 0.33 | 0.00 | 0.49 | 0.59 | 0.66 | 0.68 |\n| neutrophil | 259 | 0.99 | 1.00 | 0.99 | 0.89 | 0.00 | 0.96 | 0.99 | 0.97 | 0.99 |\n| regulatory T cell | 251 | 0.62 | 0.60 | 0.72 | 0.37 | 0.00 | 0.79 | 0.85 | 0.84 | 0.83 |\n| sebum secreting cell | 122 | 0.83 | 0.87 | 0.90 | 0.92 | 0.00 | 0.96 | 0.98 | 0.98 | 0.93 |\n| myeloid dendritic cell | 92 | 0.47 | 0.35 | 0.61 | 0.69 | 0.00 | 0.61 | 0.75 | 0.80 | 0.75 |\n| melanocyte | 91 | 0.83 | 0.80 | 0.85 | 0.81 | 0.00 | 0.87 | 0.97 | 0.95 | 0.91 |\n| plasma cell | 76 | 0.78 | 0.95 | 1.00 | 0.64 | 0.00 | 0.83 | 0.99 | 0.98 | 0.99 |\n| Langerhans cell | 68 | 0.50 | 0.50 | 0.74 | 0.60 | 0.00 | 0.48 | 0.70 | 0.81 | 0.80 |\n| natural killer cell | 61 | 0.41 | 0.08 | 0.47 | 0.29 | 0.00 | 0.61 | 0.82 | 0.84 | 0.80 |\n| mature NK T cell | 28 | 0.00 | 0.00 | 0.23 | 0.32 | 0.00 | 0.56 | 0.93 | 0.81 | 0.81 |\n| keratocyte | 12 | 0.00 | 0.00 | 0.92 | 0.64 | 0.00 | 0.69 | 1.00 | 0.96 | 1.00 |\n| basophil | 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.30 | 1.00 | 1.00 | 0.00 |\n| epithelial cell | 8 | 0.00 | 0.00 | 0.00 | 0.53 | 0.00 | 0.73 | 0.89 | 1.00 | 0.86 |\n| B cell | 7 | 0.00 | 0.20 | 0.86 | 0.62 | 0.00 | 0.56 | 1.00 | 0.93 | 1.00 |\n| erythrocyte | 5 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| stromal cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 1.00 | 0.89 | 1.00 |\n| muscle cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |\n| activated CD4-positive, alpha-beta T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 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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     "gene_names": [
         "ENSG00000001036",
         "ENSG00000001167",
+        "ENSG00000001460",
         "ENSG00000001461",
         "ENSG00000001497",
         "ENSG00000001617",
@@ -46,7 +47,6 @@
         "ENSG00000007908",
         "ENSG00000007923",
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-        "ENSG00000008282",
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         "ENSG00000035403",
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+        "ENSG00000036054",
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         "ENSG00000073861",
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+        "ENSG00000074181",
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         "ENSG00000082175",
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         "ENSG00000101082",
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         "ENSG00000103855",
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         "ENSG00000110107",
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-        "ENSG00000110315",
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         "ENSG00000111785",
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         "ENSG00000111879",
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         "ENSG00000112276",
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         "ENSG00000112367",
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         "ENSG00000121058",
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         "ENSG00000123600",
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         "ENSG00000125843",
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         "ENSG00000130021",
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         "ENSG00000130803",
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         "ENSG00000138617",
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         "ENSG00000140525",
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         "ENSG00000142733",
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         "ENSG00000146192",
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-        "ENSG00000146243",
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         "ENSG00000148481",
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         "ENSG00000153956",
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+        "ENSG00000154059",
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         "ENSG00000156239",
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         "ENSG00000159596",
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-        "ENSG00000159714",
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