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README.md

@@ -5,7 +5,10 @@ tags:
 - biology
 - genomics
 - single-cell
-- anndata_version:0.11.3
+- anndata_version:0.12.2
+- scikit_learn_version:1.7.2
+- organism:Homo sapiens
+- python_version:3.12.8
 - popV
 - 'tissue: test'
 ---
@@ -67,37 +70,37 @@ The train accuracies are computed on the training data.
 
 | Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| macrophage | 370 | 0.95 | 0.92 | 0.93 | 0.92 | 0.00 | 0.00 | 0.95 | 0.92 | 0.95 |
-| pulmonary alveolar type 2 cell | 243 | 0.98 | 0.89 | 0.93 | 0.97 | 0.00 | 0.80 | 0.99 | 0.95 | 0.98 |
-| basal cell | 59 | 0.69 | 0.21 | 0.82 | 0.78 | 0.00 | 0.00 | 0.93 | 0.91 | 0.94 |
-| non-classical monocyte | 34 | 0.46 | 0.00 | 0.26 | 0.55 | 0.00 | 0.00 | 0.67 | 0.56 | 0.63 |
-| club cell | 32 | 0.76 | 0.31 | 0.67 | 0.60 | 0.00 | 0.00 | 0.93 | 0.84 | 0.86 |
-| capillary endothelial cell | 31 | 0.76 | 0.80 | 0.93 | 0.69 | 0.00 | 0.00 | 0.98 | 0.94 | 0.95 |
-| classical monocyte | 26 | 0.69 | 0.49 | 0.74 | 0.51 | 0.00 | 0.00 | 0.98 | 0.92 | 0.92 |
-| basophil | 23 | 0.85 | 0.88 | 0.90 | 0.61 | 0.00 | 0.07 | 1.00 | 0.98 | 0.96 |
-| CD4-positive, alpha-beta T cell | 20 | 0.58 | 0.51 | 0.67 | 0.39 | 0.00 | 0.00 | 0.98 | 0.98 | 0.83 |
-| respiratory goblet cell | 18 | 0.60 | 0.45 | 0.80 | 0.67 | 0.00 | 0.00 | 0.97 | 0.88 | 0.95 |
-| vein endothelial cell | 14 | 0.44 | 0.52 | 0.72 | 0.33 | 0.00 | 0.00 | 0.90 | 0.97 | 0.88 |
-| lung microvascular endothelial cell | 14 | 0.85 | 0.61 | 0.87 | 0.69 | 0.00 | 0.00 | 1.00 | 1.00 | 0.90 |
-| lung ciliated cell | 14 | 0.85 | 0.92 | 0.88 | 0.57 | 0.00 | 0.00 | 1.00 | 0.97 | 1.00 |
-| CD8-positive, alpha-beta T cell | 12 | 0.00 | 0.00 | 0.53 | 0.59 | 0.00 | 0.00 | 0.96 | 1.00 | 0.91 |
-| fibroblast | 11 | 0.67 | 0.46 | 0.74 | 0.29 | 0.00 | 0.00 | 1.00 | 0.96 | 1.00 |
-| intermediate monocyte | 9 | 0.00 | 0.00 | 0.71 | 0.00 | 0.00 | 0.00 | 1.00 | 0.86 | 0.80 |
-| adventitial cell | 9 | 0.78 | 0.00 | 0.76 | 0.75 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
-| endothelial cell of artery | 8 | 0.00 | 0.25 | 0.80 | 0.47 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
-| pulmonary alveolar type 1 cell | 8 | 0.67 | 0.00 | 0.40 | 0.00 | 0.00 | 0.00 | 0.80 | 0.62 | 0.67 |
-| neutrophil | 7 | 0.93 | 0.25 | 0.83 | 0.92 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
-| dendritic cell | 6 | 0.50 | 0.29 | 0.25 | 0.40 | 0.00 | 0.00 | 1.00 | 0.86 | 0.80 |
-| pericyte | 6 | 0.80 | 0.00 | 0.75 | 0.67 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
-| effector CD8-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.33 | 0.86 | 0.00 | 0.00 | 1.00 | 1.00 | 0.50 |
-| effector CD4-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.00 | 0.57 | 0.00 | 0.00 | 1.00 | 1.00 | 0.80 |
-| plasma cell | 2 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
+| macrophage | 370 | 0.96 | 0.92 | 0.90 | 0.90 | 0.00 | 0.78 | 0.96 | 0.95 | 0.95 |
+| pulmonary alveolar type 2 cell | 243 | 0.97 | 0.89 | 0.89 | 0.94 | 0.00 | 0.00 | 0.99 | 0.98 | 0.97 |
+| basal cell | 59 | 0.81 | 0.21 | 0.72 | 0.69 | 0.00 | 0.11 | 0.97 | 0.87 | 0.93 |
+| non-classical monocyte | 34 | 0.50 | 0.00 | 0.00 | 0.50 | 0.00 | 0.00 | 0.72 | 0.65 | 0.65 |
+| club cell | 32 | 0.79 | 0.31 | 0.35 | 0.61 | 0.00 | 0.16 | 0.93 | 0.79 | 0.89 |
+| capillary endothelial cell | 31 | 0.78 | 0.80 | 0.84 | 0.75 | 0.00 | 0.00 | 1.00 | 0.94 | 0.89 |
+| classical monocyte | 26 | 0.69 | 0.49 | 0.46 | 0.24 | 0.00 | 0.19 | 0.95 | 0.82 | 0.94 |
+| basophil | 23 | 0.93 | 0.88 | 0.81 | 0.45 | 0.00 | 0.00 | 1.00 | 0.98 | 0.98 |
+| CD4-positive, alpha-beta T cell | 20 | 0.57 | 0.51 | 0.61 | 0.51 | 0.00 | 0.00 | 0.95 | 1.00 | 0.69 |
+| respiratory goblet cell | 18 | 0.70 | 0.45 | 0.76 | 0.09 | 0.00 | 0.00 | 0.95 | 0.84 | 0.94 |
+| vein endothelial cell | 14 | 0.00 | 0.52 | 0.67 | 0.28 | 0.00 | 0.00 | 0.97 | 1.00 | 0.83 |
+| lung microvascular endothelial cell | 14 | 0.78 | 0.61 | 0.85 | 0.34 | 0.00 | 0.00 | 1.00 | 1.00 | 0.90 |
+| lung ciliated cell | 14 | 0.88 | 0.92 | 0.73 | 0.48 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
+| CD8-positive, alpha-beta T cell | 12 | 0.14 | 0.00 | 0.15 | 0.14 | 0.00 | 0.00 | 1.00 | 1.00 | 0.59 |
+| fibroblast | 11 | 0.78 | 0.46 | 0.50 | 0.17 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
+| intermediate monocyte | 9 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.69 | 0.20 |
+| adventitial cell | 9 | 0.75 | 0.00 | 0.72 | 0.69 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
+| endothelial cell of artery | 8 | 0.00 | 0.25 | 0.40 | 0.00 | 0.00 | 0.00 | 1.00 | 0.94 | 0.55 |
+| pulmonary alveolar type 1 cell | 8 | 0.55 | 0.00 | 0.22 | 0.00 | 0.00 | 0.00 | 0.89 | 0.84 | 0.46 |
+| neutrophil | 7 | 0.88 | 0.25 | 0.83 | 0.63 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
+| dendritic cell | 6 | 0.67 | 0.29 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.92 | 0.80 |
+| pericyte | 6 | 0.67 | 0.00 | 0.80 | 0.44 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
+| 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 |
+| 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 |
+| plasma cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
 | bronchial smooth muscle cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
 | smooth muscle cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
 | endothelial cell of lymphatic vessel | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |
 | mature NK T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |
-| pulmonary ionocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 |
-| B cell | 1 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |
+| pulmonary ionocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |
+| 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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