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README.md

@@ -6,7 +6,7 @@ tags:
 - genomics
 - single-cell
 - anndata_version:0.11.3
-- python_version:3.11.11
+- python_version:3.11.12
 - popV
 - 'tissue: trachea'
 ---
@@ -32,33 +32,33 @@ computed on a 10% random subset of the data that was not used for training.
 
 | Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| fibroblast | 122 | 0.97 | 0.97 | 0.97 | 0.95 | 0.00 | 0.96 | 0.98 | 0.97 | 0.98 |
-| macrophage | 49 | 0.99 | 1.00 | 1.00 | 0.95 | 0.00 | 0.83 | 1.00 | 1.00 | 1.00 |
-| basal epithelial cell of tracheobronchial tree | 35 | 0.99 | 0.97 | 0.99 | 0.84 | 0.00 | 0.79 | 0.99 | 0.97 | 0.99 |
-| T cell | 25 | 1.00 | 0.98 | 1.00 | 0.78 | 0.00 | 0.89 | 0.98 | 1.00 | 1.00 |
-| chondrocyte | 25 | 0.90 | 0.94 | 0.90 | 0.73 | 0.00 | 0.85 | 0.94 | 0.92 | 0.92 |
-| endothelial cell | 27 | 1.00 | 0.98 | 1.00 | 1.00 | 0.00 | 0.96 | 1.00 | 0.98 | 1.00 |
-| smooth muscle cell of trachea | 10 | 0.90 | 0.75 | 0.82 | 0.91 | 0.00 | 0.78 | 0.84 | 0.89 | 0.89 |
-| mucus secreting cell | 11 | 1.00 | 1.00 | 1.00 | 0.29 | 0.00 | 0.58 | 1.00 | 1.00 | 1.00 |
-| granulocyte | 4 | 1.00 | 1.00 | 1.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |
+| fibroblast | 125 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |
+| macrophage | 49 | 0.99 | 1.00 | 1.00 | 0.93 | 0.00 | 0.73 | 1.00 | 1.00 | 1.00 |
+| basal epithelial cell of tracheobronchial tree | 35 | 0.97 | 0.96 | 0.99 | 0.82 | 0.00 | 0.74 | 0.99 | 0.96 | 0.99 |
+| T cell | 25 | 1.00 | 1.00 | 1.00 | 0.84 | 0.00 | 0.89 | 0.98 | 1.00 | 1.00 |
+| chondrocyte | 23 | 0.94 | 0.95 | 0.96 | 0.89 | 0.00 | 0.91 | 0.96 | 0.94 | 0.96 |
+| endothelial cell | 25 | 0.98 | 0.98 | 1.00 | 0.98 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |
+| smooth muscle cell of trachea | 11 | 0.90 | 0.78 | 0.84 | 0.83 | 0.00 | 0.91 | 0.86 | 0.84 | 0.84 |
+| mucus secreting cell | 11 | 0.92 | 1.00 | 1.00 | 0.40 | 0.00 | 0.83 | 1.00 | 1.00 | 1.00 |
+| granulocyte | 4 | 1.00 | 1.00 | 1.00 | 0.00 | 0.00 | 0.36 | 1.00 | 1.00 | 1.00 |
 | keratinocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| ciliated columnar cell of tracheobronchial tree | 1 | 1.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 |
+| ciliated columnar cell of tracheobronchial tree | 1 | 1.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.14 | 0.00 | 1.00 | 1.00 |
 
 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| fibroblast | 1113 | 0.98 | 0.97 | 0.98 | 0.96 | 0.00 | 0.97 | 1.00 | 0.99 | 0.99 |
-| macrophage | 381 | 0.99 | 0.99 | 0.99 | 0.95 | 0.00 | 0.87 | 1.00 | 1.00 | 1.00 |
-| basal epithelial cell of tracheobronchial tree | 365 | 0.94 | 0.93 | 0.95 | 0.87 | 0.00 | 0.84 | 1.00 | 0.99 | 0.99 |
-| T cell | 257 | 0.99 | 1.00 | 1.00 | 0.93 | 0.00 | 0.93 | 1.00 | 1.00 | 1.00 |
-| chondrocyte | 250 | 0.95 | 0.95 | 0.95 | 0.85 | 0.00 | 0.90 | 0.99 | 0.99 | 0.98 |
-| endothelial cell | 214 | 1.00 | 0.99 | 1.00 | 0.97 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |
-| smooth muscle cell of trachea | 115 | 0.84 | 0.73 | 0.92 | 0.78 | 0.00 | 0.83 | 0.99 | 0.99 | 0.94 |
-| mucus secreting cell | 62 | 0.98 | 0.97 | 0.95 | 0.51 | 0.00 | 0.69 | 1.00 | 1.00 | 0.99 |
-| granulocyte | 49 | 0.99 | 0.97 | 0.98 | 0.72 | 0.00 | 0.62 | 1.00 | 1.00 | 1.00 |
-| keratinocyte | 21 | 1.00 | 0.00 | 0.88 | 0.98 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |
-| ciliated columnar cell of tracheobronchial tree | 17 | 0.79 | 0.90 | 0.91 | 0.10 | 0.00 | 0.62 | 1.00 | 1.00 | 1.00 |
+| fibroblast | 1110 | 0.97 | 0.97 | 0.98 | 0.97 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
+| macrophage | 381 | 0.98 | 0.99 | 0.99 | 0.93 | 0.00 | 0.76 | 1.00 | 1.00 | 1.00 |
+| basal epithelial cell of tracheobronchial tree | 365 | 0.94 | 0.93 | 0.95 | 0.87 | 0.00 | 0.70 | 1.00 | 0.99 | 0.98 |
+| T cell | 257 | 1.00 | 1.00 | 0.99 | 0.92 | 0.00 | 0.93 | 1.00 | 1.00 | 1.00 |
+| chondrocyte | 252 | 0.93 | 0.94 | 0.95 | 0.90 | 0.00 | 0.94 | 0.98 | 0.98 | 0.96 |
+| endothelial cell | 216 | 1.00 | 1.00 | 1.00 | 0.99 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
+| smooth muscle cell of trachea | 114 | 0.90 | 0.72 | 0.92 | 0.75 | 0.00 | 0.77 | 1.00 | 1.00 | 0.94 |
+| mucus secreting cell | 62 | 0.95 | 0.98 | 0.99 | 0.63 | 0.00 | 0.78 | 1.00 | 1.00 | 0.99 |
+| granulocyte | 49 | 0.97 | 0.99 | 0.98 | 0.47 | 0.00 | 0.43 | 1.00 | 1.00 | 1.00 |
+| keratinocyte | 21 | 1.00 | 0.00 | 0.82 | 0.95 | 0.00 | 0.82 | 1.00 | 1.00 | 1.00 |
+| ciliated columnar cell of tracheobronchial tree | 17 | 0.83 | 0.90 | 0.94 | 0.11 | 0.00 | 0.22 | 1.00 | 1.00 | 0.97 |
 
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