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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| stromal cell of ovary | 3484 | 0.99 | 0.97 | 0.96 | 0.98 | 0.00 | 0.96 | 0.97 | 0.97 | 0.99 |\n| blood vessel smooth muscle cell | 660 | 0.97 | 0.92 | 0.95 | 0.96 | 0.00 | 0.95 | 0.95 | 0.93 | 0.97 |\n| stromal cell | 221 | 0.96 | 0.72 | 0.52 | 0.90 | 0.00 | 0.86 | 0.88 | 0.95 | 0.96 |\n| endothelial cell | 169 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| smooth muscle cell | 107 | 0.94 | 0.59 | 0.71 | 0.92 | 0.00 | 0.86 | 0.94 | 0.94 | 0.96 |\n| theca cell | 123 | 0.82 | 0.72 | 0.90 | 0.83 | 0.00 | 0.67 | 0.74 | 0.73 | 0.86 |\n| macrophage | 56 | 0.93 | 0.95 | 0.95 | 0.91 | 0.00 | 0.93 | 0.92 | 0.95 | 0.95 |\n| ovarian surface epithelial cell | 20 | 0.98 | 0.95 | 0.97 | 0.79 | 0.00 | 0.51 | 0.91 | 0.91 | 0.98 |\n| glandular epithelial cell | 27 | 0.98 | 0.90 | 0.98 | 0.82 | 0.00 | 0.93 | 0.98 | 0.95 | 1.00 |\n| CD8-positive, alpha-beta T cell | 8 | 0.57 | 0.74 | 0.63 | 0.67 | 0.00 | 0.78 | 0.80 | 0.80 | 0.70 |\n| leukocyte | 4 | 0.00 | 0.00 | 0.57 | 0.40 | 0.00 | 0.86 | 0.86 | 0.67 | 0.40 |\n| CD4-positive, alpha-beta T cell | 5 | 0.00 | 0.50 | 0.25 | 0.00 | 0.00 | 0.40 | 0.00 | 0.33 | 0.29 |\n| glial cell | 1 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.67 | 0.67 | 0.67 |\n| oocyte | 3 | 1.00 | 1.00 | 1.00 | 0.86 | 0.00 | 0.86 | 1.00 | 1.00 | 1.00 |\n| neutrophil | 2 | 0.00 | 1.00 | 1.00 | 0.67 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| plasma cell | 4 | 0.00 | 0.00 | 0.86 | 0.40 | 0.00 | 0.57 | 0.40 | 0.86 | 0.67 |\n| epithelial cell | 1 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| monocyte | 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| classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| mast cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 | 1.00 | 0.00 |\n| mature NK T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| hematopoietic precursor 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| stromal cell of ovary | 31519 | 0.98 | 0.97 | 0.98 | 0.99 | 0.00 | 0.97 | 0.97 | 0.97 | 0.99 |\n| blood vessel smooth muscle cell | 5982 | 0.97 | 0.89 | 0.97 | 0.97 | 0.00 | 0.96 | 0.95 | 0.93 | 0.98 |\n| stromal cell | 1938 | 0.95 | 0.73 | 0.73 | 0.93 | 0.00 | 0.94 | 0.90 | 0.94 | 0.98 |\n| endothelial cell | 1555 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 1.00 |\n| smooth muscle cell | 1164 | 0.96 | 0.56 | 0.85 | 0.93 | 0.00 | 0.93 | 0.96 | 0.96 | 0.98 |\n| theca cell | 915 | 0.76 | 0.59 | 0.94 | 0.86 | 0.00 | 0.68 | 0.72 | 0.68 | 0.84 |\n| macrophage | 348 | 0.89 | 0.93 | 0.96 | 0.90 | 0.00 | 0.95 | 0.98 | 0.98 | 0.98 |\n| ovarian surface epithelial cell | 221 | 0.96 | 0.95 | 0.98 | 0.89 | 0.00 | 0.57 | 0.92 | 0.91 | 1.00 |\n| glandular epithelial cell | 208 | 0.95 | 0.86 | 0.99 | 0.86 | 0.00 | 0.90 | 0.98 | 0.96 | 0.99 |\n| CD8-positive, alpha-beta T cell | 65 | 0.63 | 0.76 | 0.84 | 0.76 | 0.00 | 0.98 | 1.00 | 1.00 | 0.93 |\n| leukocyte | 23 | 0.00 | 0.30 | 0.77 | 0.73 | 0.00 | 0.96 | 1.00 | 1.00 | 0.95 |\n| CD4-positive, alpha-beta T cell | 18 | 0.00 | 0.09 | 0.39 | 0.46 | 0.00 | 0.84 | 1.00 | 1.00 | 0.80 |\n| glial cell | 19 | 0.76 | 0.10 | 0.79 | 0.61 | 0.00 | 0.17 | 0.90 | 0.83 | 0.84 |\n| oocyte | 15 | 0.88 | 0.87 | 0.87 | 0.90 | 0.00 | 0.86 | 0.81 | 0.86 | 0.88 |\n| neutrophil | 15 | 0.00 | 0.97 | 1.00 | 0.42 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |\n| plasma cell | 10 | 0.00 | 0.57 | 0.82 | 0.40 | 0.00 | 0.72 | 0.95 | 0.83 | 0.95 |\n| epithelial cell | 8 | 0.00 | 0.00 | 0.80 | 0.86 | 0.00 | 0.70 | 1.00 | 1.00 | 1.00 |\n| plasmacytoid dendritic cell | 5 | 0.00 | 0.00 | 0.60 | 0.67 | 0.00 | 0.62 | 1.00 | 1.00 | 1.00 |\n| monocyte | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.86 | 1.00 | 1.00 | 0.00 |\n| B cell | 3 | 0.00 | 0.00 | 0.80 | 0.00 | 0.00 | 0.46 | 1.00 | 1.00 | 1.00 |\n| classical monocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.21 | 1.00 | 1.00 | 0.50 |\n| mast cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.40 | 1.00 | 1.00 | 1.00 |\n| mature NK T cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.80 | 1.00 | 1.00 | 0.67 |\n| T cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.15 | 1.00 | 1.00 | 1.00 |\n| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 |\n| hematopoietic precursor cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 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| stromal cell of ovary | 3480 | 0.98 | 0.97 | 0.96 | 0.99 | 0.00 | 0.96 | 0.97 | 0.97 | 0.99 |\n| blood vessel smooth muscle cell | 658 | 0.97 | 0.92 | 0.94 | 0.95 | 0.00 | 0.96 | 0.94 | 0.91 | 0.97 |\n| stromal cell | 226 | 0.96 | 0.75 | 0.48 | 0.92 | 0.00 | 0.91 | 0.88 | 0.90 | 0.97 |\n| endothelial cell | 174 | 0.99 | 0.99 | 1.00 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| smooth muscle cell | 104 | 0.96 | 0.58 | 0.69 | 0.89 | 0.00 | 0.95 | 0.94 | 0.92 | 0.96 |\n| theca cell | 121 | 0.78 | 0.75 | 0.88 | 0.81 | 0.00 | 0.66 | 0.75 | 0.72 | 0.86 |\n| macrophage | 60 | 0.95 | 0.96 | 0.95 | 0.88 | 0.00 | 0.93 | 0.93 | 0.96 | 0.97 |\n| ovarian surface epithelial cell | 19 | 0.95 | 0.89 | 0.94 | 0.74 | 0.00 | 0.54 | 0.86 | 0.95 | 0.95 |\n| glandular epithelial cell | 28 | 0.98 | 0.94 | 0.98 | 0.81 | 0.00 | 0.90 | 0.97 | 0.97 | 0.98 |\n| CD8-positive, alpha-beta T cell | 8 | 0.67 | 0.70 | 0.63 | 0.50 | 0.00 | 0.76 | 0.89 | 0.94 | 0.84 |\n| leukocyte | 4 | 0.00 | 0.00 | 0.29 | 0.40 | 0.00 | 0.75 | 0.67 | 0.86 | 0.67 |\n| CD4-positive, alpha-beta T cell | 4 | 0.00 | 0.33 | 0.29 | 0.00 | 0.00 | 0.00 | 0.67 | 0.86 | 0.40 |\n| glial cell | 1 | 0.67 | 1.00 | 0.67 | 0.00 | 0.00 | 0.02 | 0.67 | 0.67 | 0.67 |\n| oocyte | 3 | 0.75 | 1.00 | 1.00 | 0.86 | 0.00 | 1.00 | 0.86 | 1.00 | 1.00 |\n| neutrophil | 2 | 1.00 | 1.00 | 1.00 | 0.50 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |\n| plasma cell | 3 | 0.67 | 0.00 | 0.80 | 1.00 | 0.00 | 1.00 | 1.00 | 0.80 | 1.00 |\n| epithelial cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| monocyte | 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| classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| mast cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| mature NK T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| hematopoietic precursor 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| stromal cell of ovary | 31523 | 0.98 | 0.97 | 0.98 | 0.99 | 0.00 | 0.97 | 0.97 | 0.97 | 0.99 |\n| blood vessel smooth muscle cell | 5984 | 0.97 | 0.89 | 0.97 | 0.96 | 0.00 | 0.97 | 0.95 | 0.92 | 0.98 |\n| stromal cell | 1933 | 0.96 | 0.72 | 0.72 | 0.93 | 0.00 | 0.95 | 0.90 | 0.93 | 0.98 |\n| endothelial cell | 1550 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| smooth muscle cell | 1167 | 0.97 | 0.55 | 0.84 | 0.92 | 0.00 | 0.95 | 0.96 | 0.97 | 0.98 |\n| theca cell | 917 | 0.73 | 0.62 | 0.94 | 0.84 | 0.00 | 0.64 | 0.72 | 0.71 | 0.84 |\n| macrophage | 344 | 0.90 | 0.93 | 0.96 | 0.92 | 0.00 | 0.97 | 0.96 | 0.98 | 0.98 |\n| ovarian surface epithelial cell | 222 | 0.97 | 0.95 | 0.97 | 0.92 | 0.00 | 0.67 | 0.90 | 0.96 | 1.00 |\n| glandular epithelial cell | 207 | 0.95 | 0.84 | 0.99 | 0.90 | 0.00 | 0.93 | 0.98 | 0.92 | 0.99 |\n| CD8-positive, alpha-beta T cell | 65 | 0.67 | 0.76 | 0.81 | 0.83 | 0.00 | 0.96 | 1.00 | 1.00 | 0.92 |\n| leukocyte | 23 | 0.00 | 0.30 | 0.62 | 0.75 | 0.00 | 1.00 | 1.00 | 1.00 | 0.98 |\n| CD4-positive, alpha-beta T cell | 19 | 0.00 | 0.00 | 0.45 | 0.46 | 0.00 | 0.95 | 1.00 | 1.00 | 0.73 |\n| glial cell | 19 | 0.76 | 0.00 | 0.77 | 0.57 | 0.00 | 0.06 | 0.90 | 0.84 | 0.84 |\n| oocyte | 15 | 0.62 | 0.87 | 0.85 | 0.90 | 0.00 | 0.71 | 0.83 | 0.86 | 0.83 |\n| neutrophil | 15 | 0.81 | 0.94 | 0.97 | 0.64 | 0.00 | 0.81 | 1.00 | 1.00 | 1.00 |\n| plasma cell | 11 | 0.61 | 0.53 | 0.90 | 0.80 | 0.00 | 0.83 | 0.96 | 0.81 | 0.92 |\n| epithelial cell | 8 | 0.00 | 0.00 | 0.74 | 0.57 | 0.00 | 0.73 | 1.00 | 0.94 | 1.00 |\n| plasmacytoid dendritic cell | 5 | 0.00 | 0.00 | 0.44 | 0.83 | 0.00 | 0.56 | 1.00 | 1.00 | 0.91 |\n| monocyte | 4 | 0.00 | 0.00 | 0.00 | 0.29 | 0.00 | 0.89 | 1.00 | 1.00 | 0.40 |\n| B cell | 3 | 0.00 | 0.00 | 0.50 | 0.80 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |\n| classical monocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.86 | 1.00 | 1.00 | 0.50 |\n| mast cell | 3 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |\n| mature NK T cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 0.67 |\n| T cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |\n| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 0.00 |\n| hematopoietic precursor cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.03 | 1.00 | 1.00 | 1.00 |"
 }

celltypist.pkl

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harmony_knn_classifier.joblib

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preprocessing.json

@@ -102,6 +102,7 @@
         "ENSG00000021826",
         "ENSG00000023287",
         "ENSG00000023318",
+        "ENSG00000023330",
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         "ENSG00000041880",
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         "ENSG00000063761",
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         "ENSG00000064763",
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