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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| macrophage | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| pulmonary alveolar type 2 cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| basal cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| non-classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| club cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| capillary endothelial 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| basophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| 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 |\n| respiratory goblet cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| vein endothelial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| lung microvascular endothelial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| lung ciliated cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| CD8-positive, alpha-beta T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| fibroblast | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| intermediate monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| adventitial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| endothelial cell of artery | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| pulmonary alveolar type 1 cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| neutrophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| pericyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| effector CD8-positive, alpha-beta T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| effector 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 |\n| plasma cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| bronchial smooth muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| smooth muscle cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| endothelial cell of lymphatic vessel | 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| pulmonary ionocyte | 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 |",
-    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| macrophage | 370 | 0.98 | 0.92 | 0.90 | 0.90 | 0.00 | 0.00 | 0.96 | 0.95 | 0.96 |\n| pulmonary alveolar type 2 cell | 243 | 0.97 | 0.89 | 0.89 | 0.92 | 0.00 | 0.05 | 0.98 | 0.96 | 0.97 |\n| basal cell | 59 | 0.80 | 0.21 | 0.72 | 0.74 | 0.00 | 0.00 | 0.95 | 0.93 | 0.92 |\n| non-classical monocyte | 34 | 0.48 | 0.00 | 0.00 | 0.22 | 0.00 | 0.00 | 0.68 | 0.63 | 0.54 |\n| club cell | 32 | 0.81 | 0.31 | 0.35 | 0.36 | 0.00 | 0.19 | 0.93 | 0.84 | 0.84 |\n| capillary endothelial cell | 31 | 0.78 | 0.80 | 0.84 | 0.67 | 0.00 | 0.50 | 1.00 | 0.98 | 0.85 |\n| classical monocyte | 26 | 0.66 | 0.49 | 0.46 | 0.27 | 0.00 | 0.00 | 0.88 | 0.93 | 0.94 |\n| basophil | 23 | 0.93 | 0.88 | 0.81 | 0.44 | 0.00 | 0.08 | 1.00 | 0.95 | 0.94 |\n| CD4-positive, alpha-beta T cell | 20 | 0.57 | 0.51 | 0.61 | 0.53 | 0.00 | 0.00 | 0.98 | 1.00 | 0.74 |\n| respiratory goblet cell | 18 | 0.71 | 0.45 | 0.76 | 0.10 | 0.00 | 0.00 | 0.95 | 0.95 | 0.94 |\n| vein endothelial cell | 14 | 0.00 | 0.52 | 0.67 | 0.38 | 0.00 | 0.00 | 1.00 | 0.97 | 0.73 |\n| lung microvascular endothelial cell | 14 | 0.78 | 0.61 | 0.85 | 0.55 | 0.00 | 0.00 | 1.00 | 1.00 | 0.90 |\n| lung ciliated cell | 14 | 0.88 | 0.92 | 0.73 | 0.58 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| CD8-positive, alpha-beta T cell | 12 | 0.14 | 0.00 | 0.15 | 0.32 | 0.00 | 0.00 | 0.92 | 1.00 | 0.67 |\n| fibroblast | 11 | 0.78 | 0.46 | 0.50 | 0.00 | 0.00 | 0.00 | 1.00 | 0.96 | 1.00 |\n| intermediate monocyte | 9 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.95 | 0.82 | 0.67 |\n| adventitial cell | 9 | 0.75 | 0.00 | 0.72 | 0.67 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of artery | 8 | 0.00 | 0.25 | 0.40 | 0.22 | 0.00 | 0.00 | 1.00 | 0.94 | 0.40 |\n| pulmonary alveolar type 1 cell | 8 | 0.55 | 0.00 | 0.22 | 0.00 | 0.00 | 0.00 | 0.84 | 0.62 | 0.46 |\n| neutrophil | 7 | 0.88 | 0.25 | 0.83 | 0.83 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| dendritic cell | 6 | 0.67 | 0.29 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.92 | 0.91 |\n| pericyte | 6 | 0.67 | 0.00 | 0.80 | 0.67 | 0.00 | 0.00 | 1.00 | 0.92 | 1.00 |\n| effector CD8-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 |\n| effector CD4-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 |\n| plasma cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| bronchial smooth muscle cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| smooth muscle cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of lymphatic vessel | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |\n| mature NK T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |\n| pulmonary ionocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |\n| B cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 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| macrophage | 370 | 0.98 | 0.92 | 0.90 | 0.92 | 0.00 | 0.00 | 0.98 | 0.97 | 0.96 |\n| pulmonary alveolar type 2 cell | 243 | 0.97 | 0.89 | 0.89 | 0.93 | 0.00 | 0.04 | 0.98 | 0.95 | 0.98 |\n| basal cell | 59 | 0.80 | 0.21 | 0.72 | 0.70 | 0.00 | 0.00 | 0.93 | 0.92 | 0.93 |\n| non-classical monocyte | 34 | 0.60 | 0.00 | 0.00 | 0.37 | 0.00 | 0.00 | 0.86 | 0.79 | 0.77 |\n| club cell | 32 | 0.79 | 0.31 | 0.35 | 0.58 | 0.00 | 0.10 | 0.91 | 0.78 | 0.90 |\n| capillary endothelial cell | 31 | 0.77 | 0.80 | 0.84 | 0.86 | 0.00 | 0.00 | 0.98 | 0.95 | 0.90 |\n| classical monocyte | 26 | 0.69 | 0.49 | 0.46 | 0.46 | 0.00 | 0.00 | 0.96 | 0.98 | 0.98 |\n| basophil | 23 | 0.93 | 0.88 | 0.81 | 0.68 | 0.00 | 0.11 | 1.00 | 0.98 | 0.94 |\n| CD4-positive, alpha-beta T cell | 20 | 0.58 | 0.51 | 0.61 | 0.49 | 0.00 | 0.00 | 0.95 | 1.00 | 0.71 |\n| respiratory goblet cell | 18 | 0.70 | 0.45 | 0.76 | 0.19 | 0.00 | 0.00 | 0.92 | 0.90 | 0.89 |\n| vein endothelial cell | 14 | 0.00 | 0.52 | 0.67 | 0.00 | 0.00 | 0.00 | 1.00 | 0.90 | 0.73 |\n| lung microvascular endothelial cell | 14 | 0.78 | 0.61 | 0.85 | 0.51 | 0.00 | 0.00 | 1.00 | 1.00 | 0.88 |\n| lung ciliated cell | 14 | 0.88 | 0.92 | 0.73 | 0.56 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| CD8-positive, alpha-beta T cell | 12 | 0.00 | 0.00 | 0.15 | 0.12 | 0.00 | 0.00 | 0.96 | 1.00 | 0.59 |\n| fibroblast | 11 | 0.78 | 0.46 | 0.50 | 0.31 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| intermediate monocyte | 9 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.86 | 0.36 |\n| adventitial cell | 9 | 0.75 | 0.00 | 0.72 | 0.64 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of artery | 8 | 0.20 | 0.25 | 0.40 | 0.18 | 0.00 | 0.00 | 1.00 | 1.00 | 0.67 |\n| pulmonary alveolar type 1 cell | 8 | 0.55 | 0.00 | 0.22 | 0.00 | 0.00 | 0.00 | 0.89 | 0.67 | 0.50 |\n| neutrophil | 7 | 0.88 | 0.25 | 0.83 | 0.86 | 0.00 | 0.00 | 1.00 | 0.93 | 1.00 |\n| dendritic cell | 6 | 0.67 | 0.29 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.86 | 0.91 |\n| pericyte | 6 | 0.67 | 0.00 | 0.80 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| effector CD8-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.00 |\n| effector CD4-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.50 |\n| plasma cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 0.67 |\n| bronchial smooth muscle cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| smooth muscle cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |\n| endothelial cell of lymphatic vessel | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |\n| mature NK T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |\n| pulmonary ionocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |\n| B cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |"
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celltypist.pkl

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metadata.json

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-{
-    "popv_version": "0.5.3",
-    "anndata_version": "0.12.2",
-    "scikit_learn_version": "1.7.2",
-    "setup_dict": {
-        "ref_labels_key": "cell_ontology_class",
-        "ref_batch_key": "donor_assay",
-        "unknown_celltype_label": "unknown"
-    },
-    "prediction_keys": [
-        "popv_celltypist_prediction",
-        "popv_knn_bbknn_prediction",
-        "popv_knn_harmony_prediction",
-        "popv_knn_on_scvi_prediction",
-        "popv_onclass_prediction",
-        "popv_scanvi_prediction",
-        "popv_svm_prediction",
-        "popv_xgboost_prediction"
-    ],
-    "method_kwargs": {},
-    "methods": [
-        "CELLTYPIST",
-        "KNN_BBKNN",
-        "KNN_HARMONY",
-        "KNN_SCVI",
-        "ONCLASS",
-        "SCANVI_POPV",
-        "Support_Vector",
-        "XGboost"
-    ],
-    "cellxgene_url": "test",
-    "organism": null
-}

minified_ref_adata.h5ad

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scanvi/model.pt

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scvi/model.pt

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svm_classifier.joblib

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xgboost_classifier.model

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