popV
/

tabula_sapiens_Trachea

@@ -5,7 +5,8 @@ tags:
 - biology
 - genomics
 - single-cell
-- anndata_version:0.11.1
 - popV
 - 'tissue: Trachea'
 ---
@@ -31,31 +32,31 @@ 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| basal cell | 1025 | 0.98 | 0.99 | 0.98 | 0.99 | 0.00 | 0.95 | 0.98 | 0.97 | 0.99 |
-| neutrophil | 452 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.94 | 0.99 | 0.99 | 0.99 |
-| fibroblast | 178 | 0.96 | 0.96 | 0.96 | 0.97 | 0.00 | 0.95 | 0.98 | 0.97 | 0.98 |
-| CD8-positive, alpha-beta T cell | 127 | 0.92 | 0.92 | 0.91 | 0.88 | 0.00 | 0.93 | 0.94 | 0.95 | 0.95 |
-| ciliated columnar cell of tracheobronchial tree | 68 | 0.96 | 0.97 | 0.92 | 0.98 | 0.00 | 0.86 | 0.96 | 0.96 | 0.96 |
-| macrophage | 65 | 0.96 | 0.98 | 0.94 | 0.97 | 0.00 | 0.92 | 0.97 | 0.96 | 0.98 |
-| B cell | 66 | 0.98 | 0.97 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.99 | 0.99 |
-| endothelial cell | 49 | 0.97 | 0.96 | 0.97 | 0.96 | 0.00 | 0.96 | 0.99 | 0.97 | 0.97 |
-| serous cell of epithelium of trachea | 27 | 0.43 | 0.07 | 0.73 | 0.65 | 0.00 | 0.56 | 0.53 | 0.48 | 0.64 |
-| plasma cell | 31 | 0.97 | 0.97 | 0.93 | 0.95 | 0.00 | 0.95 | 0.94 | 0.95 | 0.95 |
-| CD4-positive, alpha-beta T cell | 33 | 0.85 | 0.66 | 0.76 | 0.61 | 0.00 | 0.78 | 0.83 | 0.86 | 0.82 |
-| mucus secreting cell | 34 | 0.76 | 0.83 | 0.84 | 0.83 | 0.00 | 0.71 | 0.79 | 0.79 | 0.82 |
-| tracheal goblet cell | 34 | 0.71 | 0.73 | 0.86 | 0.84 | 0.00 | 0.80 | 0.92 | 0.91 | 0.96 |
-| connective tissue cell | 10 | 0.91 | 0.00 | 0.91 | 0.67 | 0.00 | 0.91 | 0.95 | 0.91 | 1.00 |
-| smooth muscle cell | 18 | 0.81 | 0.86 | 0.77 | 0.89 | 0.00 | 0.80 | 0.85 | 0.81 | 0.83 |
-| mast cell | 19 | 0.97 | 0.97 | 1.00 | 1.00 | 0.00 | 0.97 | 0.97 | 0.97 | 0.97 |
-| monocyte | 6 | 0.77 | 0.83 | 0.71 | 0.73 | 0.00 | 0.67 | 1.00 | 0.83 | 0.91 |
-| natural killer cell | 8 | 0.57 | 0.75 | 0.80 | 0.18 | 0.00 | 0.82 | 0.74 | 0.80 | 0.82 |
-| granulocyte | 5 | 0.00 | 0.00 | 0.33 | 0.33 | 0.00 | 0.15 | 0.44 | 0.33 | 0.33 |
-| mature NK T cell | 5 | 0.25 | 0.00 | 0.67 | 0.33 | 0.00 | 0.67 | 0.80 | 0.73 | 0.80 |
 | T cell | 2 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| ionocyte | 1 | 0.00 | 0.00 | 1.00 | 0.67 | 0.00 | 0.11 | 0.67 | 1.00 | 1.00 |
 | regulatory T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| intermediate monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
-| non-classical monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
@@ -64,34 +65,34 @@ 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 |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| basal cell | 9222 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.96 | 0.98 | 0.98 | 0.99 |
-| neutrophil | 4232 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.95 | 0.99 | 0.99 | 1.00 |
-| fibroblast | 1622 | 0.95 | 0.93 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |
-| CD8-positive, alpha-beta T cell | 1075 | 0.89 | 0.91 | 0.94 | 0.90 | 0.00 | 0.96 | 0.98 | 0.98 | 0.96 |
-| ciliated columnar cell of tracheobronchial tree | 645 | 0.97 | 0.97 | 0.96 | 0.99 | 0.00 | 0.92 | 0.98 | 0.97 | 0.98 |
-| macrophage | 647 | 0.92 | 0.91 | 0.95 | 0.94 | 0.00 | 0.94 | 0.98 | 0.99 | 0.97 |
-| B cell | 561 | 0.97 | 0.95 | 0.97 | 0.98 | 0.00 | 0.98 | 1.00 | 1.00 | 0.99 |
-| endothelial cell | 537 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.97 | 1.00 | 0.99 | 0.99 |
-| serous cell of epithelium of trachea | 299 | 0.57 | 0.02 | 0.89 | 0.86 | 0.00 | 0.75 | 0.76 | 0.75 | 0.89 |
-| plasma cell | 261 | 0.97 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 1.00 | 0.99 | 1.00 |
-| CD4-positive, alpha-beta T cell | 245 | 0.73 | 0.63 | 0.78 | 0.63 | 0.00 | 0.88 | 0.94 | 0.96 | 0.84 |
-| mucus secreting cell | 236 | 0.72 | 0.72 | 0.89 | 0.85 | 0.00 | 0.73 | 0.85 | 0.85 | 0.89 |
-| tracheal goblet cell | 198 | 0.65 | 0.51 | 0.88 | 0.85 | 0.00 | 0.73 | 0.93 | 0.88 | 0.96 |
-| connective tissue cell | 142 | 0.79 | 0.00 | 0.94 | 0.96 | 0.00 | 0.97 | 0.96 | 0.96 | 0.98 |
-| smooth muscle cell | 113 | 0.80 | 0.74 | 0.87 | 0.90 | 0.00 | 0.78 | 0.95 | 0.94 | 0.88 |
-| mast cell | 100 | 0.96 | 0.96 | 0.95 | 0.99 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |
-| monocyte | 75 | 0.58 | 0.47 | 0.69 | 0.67 | 0.00 | 0.80 | 0.93 | 0.96 | 0.83 |
-| natural killer cell | 56 | 0.51 | 0.61 | 0.73 | 0.36 | 0.00 | 0.81 | 0.87 | 0.93 | 0.89 |
-| granulocyte | 34 | 0.00 | 0.00 | 0.15 | 0.11 | 0.00 | 0.16 | 0.58 | 0.62 | 0.15 |
-| mature NK T cell | 32 | 0.28 | 0.11 | 0.63 | 0.55 | 0.00 | 0.67 | 0.94 | 0.97 | 0.92 |
-| T cell | 17 | 0.00 | 0.00 | 0.69 | 0.29 | 0.00 | 0.47 | 1.00 | 0.97 | 0.94 |
-| ionocyte | 17 | 0.00 | 0.00 | 0.84 | 0.82 | 0.00 | 0.62 | 1.00 | 0.97 | 1.00 |
-| regulatory T cell | 14 | 0.00 | 0.00 | 0.32 | 0.00 | 0.00 | 0.79 | 1.00 | 1.00 | 0.60 |
-| intermediate monocyte | 15 | 0.00 | 0.00 | 0.52 | 0.45 | 0.00 | 0.60 | 1.00 | 1.00 | 0.89 |
-| non-classical monocyte | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.47 | 1.00 | 1.00 | 0.40 |
-| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
 | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
-| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.67 | 1.00 | 1.00 |
 </details>

 - biology
 - genomics
 - single-cell
+- anndata_version:0.11.3
+- python_version:3.11.11
 - popV
 - 'tissue: Trachea'
 ---
 | Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| basal cell | 1035 | 0.99 | 0.98 | 0.98 | 0.99 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |
+| neutrophil | 450 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |
+| fibroblast | 173 | 0.97 | 0.95 | 0.97 | 0.95 | 0.00 | 0.98 | 0.97 | 0.97 | 0.98 |
+| CD8-positive, alpha-beta T cell | 128 | 0.90 | 0.93 | 0.92 | 0.83 | 0.00 | 0.93 | 0.94 | 0.95 | 0.93 |
+| ciliated columnar cell of tracheobronchial tree | 74 | 0.95 | 0.97 | 0.95 | 0.98 | 0.00 | 0.95 | 0.96 | 0.96 | 0.96 |
+| macrophage | 74 | 0.97 | 0.99 | 0.97 | 0.96 | 0.00 | 0.92 | 0.99 | 0.97 | 0.98 |
+| B cell | 65 | 0.98 | 0.98 | 0.97 | 0.95 | 0.00 | 0.98 | 0.99 | 1.00 | 0.99 |
+| endothelial cell | 48 | 0.97 | 0.96 | 0.94 | 0.96 | 0.00 | 0.95 | 0.99 | 0.97 | 0.96 |
+| serous cell of epithelium of trachea | 33 | 0.72 | 0.17 | 0.82 | 0.74 | 0.00 | 0.63 | 0.68 | 0.64 | 0.83 |
+| plasma cell | 21 | 0.95 | 0.93 | 0.90 | 0.88 | 0.00 | 0.95 | 0.95 | 0.93 | 0.93 |
+| CD4-positive, alpha-beta T cell | 31 | 0.82 | 0.79 | 0.78 | 0.35 | 0.00 | 0.84 | 0.81 | 0.87 | 0.89 |
+| mucus secreting cell | 31 | 0.78 | 0.79 | 0.86 | 0.80 | 0.00 | 0.79 | 0.77 | 0.77 | 0.85 |
+| tracheal goblet cell | 33 | 0.76 | 0.68 | 0.92 | 0.82 | 0.00 | 0.87 | 0.88 | 0.86 | 0.89 |
+| connective tissue cell | 11 | 0.87 | 0.00 | 0.92 | 0.20 | 0.00 | 0.92 | 0.92 | 0.85 | 1.00 |
+| smooth muscle cell | 13 | 0.80 | 0.81 | 0.79 | 0.92 | 0.00 | 0.80 | 0.80 | 0.83 | 0.80 |
+| mast cell | 16 | 0.97 | 0.97 | 0.94 | 0.97 | 0.00 | 0.97 | 1.00 | 1.00 | 0.97 |
+| monocyte | 5 | 0.80 | 0.89 | 0.73 | 0.29 | 0.00 | 0.67 | 1.00 | 0.73 | 0.80 |
+| natural killer cell | 9 | 0.00 | 0.78 | 0.78 | 0.43 | 0.00 | 0.72 | 0.80 | 0.73 | 0.80 |
+| granulocyte | 6 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 | 0.32 | 0.53 | 0.53 | 0.29 |
+| mature NK T cell | 5 | 0.25 | 0.00 | 0.57 | 0.29 | 0.00 | 0.50 | 0.80 | 0.91 | 0.29 |
 | T cell | 2 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| ionocyte | 1 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.25 | 1.00 | 1.00 | 1.00 |
 | regulatory T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| intermediate monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
+| non-classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 | Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
 | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
+| basal cell | 9212 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |
+| neutrophil | 4234 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 1.00 |
+| fibroblast | 1627 | 0.96 | 0.93 | 0.98 | 0.98 | 0.00 | 0.97 | 0.99 | 0.98 | 0.99 |
+| CD8-positive, alpha-beta T cell | 1074 | 0.90 | 0.91 | 0.94 | 0.89 | 0.00 | 0.97 | 0.97 | 0.98 | 0.95 |
+| ciliated columnar cell of tracheobronchial tree | 639 | 0.97 | 0.97 | 0.96 | 0.99 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |
+| macrophage | 638 | 0.92 | 0.92 | 0.95 | 0.93 | 0.00 | 0.94 | 0.98 | 0.99 | 0.97 |
+| B cell | 562 | 0.96 | 0.96 | 0.98 | 0.95 | 0.00 | 0.98 | 0.99 | 1.00 | 0.99 |
+| endothelial cell | 538 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.97 | 1.00 | 0.99 | 0.99 |
+| serous cell of epithelium of trachea | 293 | 0.72 | 0.01 | 0.89 | 0.87 | 0.00 | 0.66 | 0.78 | 0.80 | 0.91 |
+| plasma cell | 271 | 0.97 | 0.98 | 0.99 | 0.93 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |
+| CD4-positive, alpha-beta T cell | 247 | 0.72 | 0.62 | 0.78 | 0.55 | 0.00 | 0.90 | 0.92 | 0.95 | 0.84 |
+| mucus secreting cell | 239 | 0.76 | 0.73 | 0.90 | 0.88 | 0.00 | 0.86 | 0.86 | 0.86 | 0.92 |
+| tracheal goblet cell | 199 | 0.69 | 0.49 | 0.88 | 0.86 | 0.00 | 0.87 | 0.90 | 0.84 | 0.93 |
+| connective tissue cell | 141 | 0.74 | 0.00 | 0.94 | 0.94 | 0.00 | 0.93 | 0.98 | 0.94 | 0.97 |
+| smooth muscle cell | 118 | 0.81 | 0.75 | 0.87 | 0.85 | 0.00 | 0.87 | 0.91 | 0.89 | 0.89 |
+| mast cell | 103 | 0.96 | 0.96 | 0.96 | 0.99 | 0.00 | 0.94 | 1.00 | 1.00 | 1.00 |
+| monocyte | 76 | 0.60 | 0.44 | 0.71 | 0.56 | 0.00 | 0.79 | 0.97 | 0.99 | 0.84 |
+| natural killer cell | 55 | 0.00 | 0.65 | 0.75 | 0.50 | 0.00 | 0.83 | 0.89 | 0.91 | 0.86 |
+| granulocyte | 33 | 0.00 | 0.00 | 0.11 | 0.16 | 0.00 | 0.31 | 0.71 | 0.72 | 0.21 |
+| mature NK T cell | 32 | 0.28 | 0.06 | 0.69 | 0.42 | 0.00 | 0.89 | 0.94 | 0.97 | 0.76 |
+| T cell | 17 | 0.00 | 0.11 | 0.57 | 0.21 | 0.00 | 0.80 | 1.00 | 0.97 | 0.97 |
+| ionocyte | 17 | 0.00 | 0.00 | 0.87 | 0.52 | 0.00 | 0.38 | 1.00 | 1.00 | 0.97 |
+| regulatory T cell | 14 | 0.00 | 0.00 | 0.42 | 0.00 | 0.00 | 0.74 | 1.00 | 1.00 | 0.67 |
+| intermediate monocyte | 15 | 0.00 | 0.00 | 0.50 | 0.25 | 0.00 | 0.36 | 1.00 | 1.00 | 0.80 |
+| non-classical monocyte | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.91 | 1.00 | 0.33 |
+| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 0.00 |
 | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
+| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.25 | 1.00 | 1.00 | 1.00 |
 </details>