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tabula_sapiens_Bone_Marrow

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biology
genomics
single-cell
anndata_version:0.11.1
tissue: Bone_Marrow
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@@ -31,61 +31,61 @@ computed on a 10% random subset of the data that was not used for training.
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  | Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
33
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
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- | neutrophil | 855 | 0.95 | 0.96 | 0.95 | 0.92 | 0.00 | 0.92 | 0.93 | 0.93 | 0.97 |
35
- | CD4-positive, alpha-beta T cell | 304 | 0.86 | 0.87 | 0.86 | 0.80 | 0.00 | 0.83 | 0.79 | 0.86 | 0.88 |
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- | CD8-positive, alpha-beta T cell | 239 | 0.82 | 0.83 | 0.80 | 0.68 | 0.00 | 0.78 | 0.72 | 0.82 | 0.83 |
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- | monocyte | 208 | 0.73 | 0.75 | 0.79 | 0.74 | 0.00 | 0.71 | 0.64 | 0.72 | 0.79 |
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- | B cell | 193 | 0.97 | 0.99 | 0.98 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
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- | hematopoietic precursor cell | 180 | 0.80 | 0.83 | 0.79 | 0.81 | 0.00 | 0.82 | 0.83 | 0.84 | 0.87 |
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- | plasma cell | 154 | 0.98 | 0.97 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |
41
- | natural killer cell | 102 | 0.93 | 0.93 | 0.91 | 0.82 | 0.00 | 0.87 | 0.92 | 0.91 | 0.94 |
42
- | erythroid progenitor cell | 108 | 0.73 | 0.79 | 0.77 | 0.76 | 0.00 | 0.75 | 0.79 | 0.86 | 0.86 |
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- | hematopoietic stem cell | 81 | 0.78 | 0.83 | 0.84 | 0.84 | 0.00 | 0.91 | 0.86 | 0.89 | 0.87 |
44
- | granulocyte | 74 | 0.69 | 0.40 | 0.57 | 0.41 | 0.00 | 0.50 | 0.63 | 0.61 | 0.80 |
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- | erythrocyte | 45 | 0.61 | 0.62 | 0.68 | 0.67 | 0.00 | 0.59 | 0.78 | 0.82 | 0.77 |
46
- | common myeloid progenitor | 45 | 0.76 | 0.72 | 0.71 | 0.57 | 0.00 | 0.67 | 0.74 | 0.81 | 0.76 |
47
- | macrophage | 31 | 0.59 | 0.39 | 0.52 | 0.42 | 0.00 | 0.49 | 0.61 | 0.67 | 0.69 |
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- | classical monocyte | 25 | 0.00 | 0.00 | 0.00 | 0.06 | 0.00 | 0.12 | 0.14 | 0.16 | 0.00 |
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- | intermediate monocyte | 25 | 0.42 | 0.47 | 0.33 | 0.27 | 0.00 | 0.39 | 0.39 | 0.38 | 0.49 |
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- | myeloid dendritic cell | 10 | 0.62 | 0.27 | 0.50 | 0.47 | 0.00 | 0.34 | 0.48 | 0.80 | 0.64 |
51
- | T cell | 11 | 0.48 | 0.00 | 0.31 | 0.13 | 0.00 | 0.41 | 0.53 | 0.62 | 0.56 |
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- | mature NK T cell | 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.36 | 0.20 | 0.22 |
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- | non-classical monocyte | 9 | 0.00 | 0.00 | 0.33 | 0.00 | 0.00 | 0.11 | 0.27 | 0.13 | 0.20 |
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- | basophil | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.00 | 0.00 | 0.00 |
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  | regulatory T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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- | fibroblast | 1 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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- | plasmacytoid dendritic cell | 4 | 0.00 | 0.00 | 0.40 | 0.40 | 0.00 | 0.80 | 0.00 | 0.40 | 0.00 |
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  | endothelial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
59
 
60
  The train accuracies are computed on the training data.
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62
  | Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
63
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
64
- | neutrophil | 7822 | 0.95 | 0.95 | 0.97 | 0.97 | 0.00 | 0.96 | 0.94 | 0.95 | 0.98 |
65
- | CD4-positive, alpha-beta T cell | 2869 | 0.84 | 0.85 | 0.87 | 0.85 | 0.00 | 0.83 | 0.85 | 0.87 | 0.88 |
66
- | CD8-positive, alpha-beta T cell | 2397 | 0.80 | 0.81 | 0.86 | 0.79 | 0.00 | 0.80 | 0.80 | 0.85 | 0.86 |
67
- | monocyte | 1832 | 0.74 | 0.78 | 0.84 | 0.82 | 0.00 | 0.76 | 0.79 | 0.85 | 0.88 |
68
- | B cell | 1626 | 0.98 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
69
- | hematopoietic precursor cell | 1540 | 0.80 | 0.83 | 0.88 | 0.87 | 0.00 | 0.86 | 0.86 | 0.88 | 0.91 |
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- | plasma cell | 1294 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 1.00 | 0.99 | 0.99 |
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- | natural killer cell | 997 | 0.92 | 0.91 | 0.94 | 0.87 | 0.00 | 0.89 | 0.94 | 0.95 | 0.97 |
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- | erythroid progenitor cell | 863 | 0.71 | 0.74 | 0.78 | 0.84 | 0.00 | 0.86 | 0.90 | 0.94 | 0.94 |
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- | hematopoietic stem cell | 711 | 0.78 | 0.82 | 0.87 | 0.87 | 0.00 | 0.88 | 0.93 | 0.94 | 0.92 |
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- | granulocyte | 561 | 0.62 | 0.25 | 0.75 | 0.66 | 0.00 | 0.65 | 0.64 | 0.64 | 0.83 |
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- | erythrocyte | 408 | 0.65 | 0.67 | 0.78 | 0.83 | 0.00 | 0.91 | 0.94 | 0.95 | 0.92 |
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- | common myeloid progenitor | 408 | 0.68 | 0.64 | 0.70 | 0.80 | 0.00 | 0.81 | 0.90 | 0.93 | 0.92 |
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- | macrophage | 327 | 0.60 | 0.47 | 0.70 | 0.69 | 0.00 | 0.85 | 0.88 | 0.90 | 0.93 |
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- | classical monocyte | 206 | 0.06 | 0.02 | 0.27 | 0.42 | 0.00 | 0.61 | 0.70 | 0.75 | 0.75 |
79
- | intermediate monocyte | 199 | 0.46 | 0.30 | 0.61 | 0.55 | 0.00 | 0.75 | 0.85 | 0.93 | 0.84 |
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- | myeloid dendritic cell | 98 | 0.57 | 0.43 | 0.72 | 0.68 | 0.00 | 0.63 | 0.73 | 0.86 | 0.89 |
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- | T cell | 87 | 0.35 | 0.00 | 0.33 | 0.34 | 0.00 | 0.42 | 0.63 | 0.63 | 0.63 |
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- | mature NK T cell | 57 | 0.00 | 0.03 | 0.29 | 0.12 | 0.00 | 0.53 | 0.93 | 0.93 | 0.92 |
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- | non-classical monocyte | 44 | 0.00 | 0.12 | 0.29 | 0.22 | 0.00 | 0.60 | 0.93 | 0.97 | 0.82 |
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- | basophil | 22 | 0.00 | 0.00 | 0.60 | 0.55 | 0.00 | 0.27 | 0.81 | 0.73 | 0.81 |
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- | regulatory T cell | 14 | 0.00 | 0.00 | 0.25 | 0.00 | 0.00 | 0.29 | 0.76 | 0.62 | 0.25 |
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- | fibroblast | 10 | 0.00 | 0.29 | 0.60 | 0.64 | 0.00 | 0.29 | 0.91 | 0.91 | 0.91 |
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- | plasmacytoid dendritic cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.25 | 0.91 | 1.00 | 0.91 |
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- | endothelial cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.80 | 1.00 | 1.00 | 0.80 |
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90
  </details>
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31
 
32
  | Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
33
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
34
+ | neutrophil | 856 | 0.96 | 0.96 | 0.96 | 0.94 | 0.00 | 0.92 | 0.95 | 0.94 | 0.97 |
35
+ | CD4-positive, alpha-beta T cell | 303 | 0.86 | 0.87 | 0.85 | 0.84 | 0.00 | 0.76 | 0.87 | 0.90 | 0.89 |
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+ | CD8-positive, alpha-beta T cell | 247 | 0.82 | 0.86 | 0.81 | 0.77 | 0.00 | 0.78 | 0.84 | 0.87 | 0.86 |
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+ | monocyte | 214 | 0.75 | 0.81 | 0.80 | 0.80 | 0.00 | 0.66 | 0.65 | 0.75 | 0.80 |
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+ | B cell | 187 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
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+ | hematopoietic precursor cell | 182 | 0.80 | 0.86 | 0.85 | 0.87 | 0.00 | 0.86 | 0.83 | 0.86 | 0.88 |
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+ | plasma cell | 149 | 0.99 | 0.99 | 1.00 | 0.99 | 0.00 | 1.00 | 0.99 | 0.99 | 1.00 |
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+ | natural killer cell | 102 | 0.93 | 0.97 | 0.95 | 0.89 | 0.00 | 0.92 | 0.95 | 0.94 | 0.95 |
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+ | erythroid progenitor cell | 107 | 0.73 | 0.77 | 0.74 | 0.76 | 0.00 | 0.75 | 0.83 | 0.87 | 0.85 |
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+ | hematopoietic stem cell | 79 | 0.77 | 0.85 | 0.83 | 0.83 | 0.00 | 0.86 | 0.86 | 0.89 | 0.90 |
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+ | granulocyte | 74 | 0.73 | 0.37 | 0.64 | 0.45 | 0.00 | 0.49 | 0.65 | 0.65 | 0.75 |
45
+ | erythrocyte | 46 | 0.57 | 0.64 | 0.66 | 0.64 | 0.00 | 0.52 | 0.82 | 0.80 | 0.75 |
46
+ | common myeloid progenitor | 44 | 0.69 | 0.73 | 0.62 | 0.62 | 0.00 | 0.67 | 0.81 | 0.86 | 0.78 |
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+ | macrophage | 31 | 0.55 | 0.49 | 0.53 | 0.43 | 0.00 | 0.62 | 0.54 | 0.65 | 0.70 |
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+ | classical monocyte | 25 | 0.10 | 0.00 | 0.16 | 0.11 | 0.00 | 0.20 | 0.18 | 0.20 | 0.11 |
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+ | intermediate monocyte | 24 | 0.34 | 0.49 | 0.41 | 0.22 | 0.00 | 0.36 | 0.43 | 0.52 | 0.57 |
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+ | myeloid dendritic cell | 10 | 0.75 | 0.27 | 0.71 | 0.84 | 0.00 | 0.67 | 0.43 | 0.61 | 0.82 |
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+ | T cell | 11 | 0.62 | 0.00 | 0.29 | 0.00 | 0.00 | 0.49 | 0.61 | 0.67 | 0.64 |
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+ | mature NK T cell | 6 | 0.00 | 0.80 | 0.44 | 0.00 | 0.00 | 0.56 | 0.33 | 0.22 | 0.25 |
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+ | non-classical monocyte | 9 | 0.00 | 0.20 | 0.18 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.00 |
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+ | basophil | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.20 | 0.00 | 0.00 | 0.00 |
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  | regulatory T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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+ | fibroblast | 1 | 0.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.67 | 0.00 | 0.00 | 1.00 |
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+ | plasmacytoid dendritic cell | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.57 | 0.00 |
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  | endothelial cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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60
  The train accuracies are computed on the training data.
61
 
62
  | Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
63
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
64
+ | neutrophil | 7821 | 0.97 | 0.96 | 0.98 | 0.98 | 0.00 | 0.97 | 0.96 | 0.95 | 0.98 |
65
+ | CD4-positive, alpha-beta T cell | 2870 | 0.85 | 0.86 | 0.89 | 0.87 | 0.00 | 0.77 | 0.89 | 0.92 | 0.90 |
66
+ | CD8-positive, alpha-beta T cell | 2389 | 0.82 | 0.83 | 0.88 | 0.83 | 0.00 | 0.79 | 0.87 | 0.89 | 0.88 |
67
+ | monocyte | 1826 | 0.78 | 0.81 | 0.87 | 0.86 | 0.00 | 0.74 | 0.82 | 0.87 | 0.89 |
68
+ | B cell | 1632 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
69
+ | hematopoietic precursor cell | 1538 | 0.80 | 0.84 | 0.91 | 0.91 | 0.00 | 0.89 | 0.87 | 0.90 | 0.92 |
70
+ | plasma cell | 1299 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |
71
+ | natural killer cell | 997 | 0.94 | 0.94 | 0.96 | 0.91 | 0.00 | 0.92 | 0.97 | 0.96 | 0.97 |
72
+ | erythroid progenitor cell | 864 | 0.70 | 0.74 | 0.82 | 0.83 | 0.00 | 0.88 | 0.93 | 0.95 | 0.94 |
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+ | hematopoietic stem cell | 713 | 0.77 | 0.83 | 0.88 | 0.88 | 0.00 | 0.88 | 0.94 | 0.95 | 0.94 |
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+ | granulocyte | 561 | 0.70 | 0.24 | 0.79 | 0.68 | 0.00 | 0.69 | 0.70 | 0.68 | 0.85 |
75
+ | erythrocyte | 407 | 0.65 | 0.65 | 0.80 | 0.79 | 0.00 | 0.87 | 0.94 | 0.95 | 0.92 |
76
+ | common myeloid progenitor | 409 | 0.61 | 0.69 | 0.77 | 0.80 | 0.00 | 0.82 | 0.92 | 0.95 | 0.91 |
77
+ | macrophage | 327 | 0.59 | 0.54 | 0.75 | 0.70 | 0.00 | 0.82 | 0.89 | 0.91 | 0.91 |
78
+ | classical monocyte | 206 | 0.21 | 0.01 | 0.38 | 0.38 | 0.00 | 0.53 | 0.70 | 0.78 | 0.75 |
79
+ | intermediate monocyte | 200 | 0.44 | 0.45 | 0.64 | 0.60 | 0.00 | 0.70 | 0.85 | 0.92 | 0.82 |
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+ | myeloid dendritic cell | 98 | 0.57 | 0.47 | 0.72 | 0.72 | 0.00 | 0.72 | 0.72 | 0.83 | 0.88 |
81
+ | T cell | 87 | 0.46 | 0.14 | 0.53 | 0.47 | 0.00 | 0.47 | 0.71 | 0.71 | 0.76 |
82
+ | mature NK T cell | 58 | 0.00 | 0.44 | 0.56 | 0.34 | 0.00 | 0.64 | 0.91 | 0.94 | 0.95 |
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+ | non-classical monocyte | 44 | 0.00 | 0.08 | 0.49 | 0.23 | 0.00 | 0.84 | 0.97 | 0.95 | 0.80 |
84
+ | basophil | 22 | 0.00 | 0.00 | 0.67 | 0.69 | 0.00 | 0.45 | 0.86 | 0.83 | 0.81 |
85
+ | regulatory T cell | 14 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.72 | 0.93 | 0.74 | 0.25 |
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+ | fibroblast | 10 | 0.00 | 0.31 | 0.67 | 0.17 | 0.00 | 0.62 | 0.91 | 0.95 | 0.82 |
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+ | plasmacytoid dendritic cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.26 | 0.91 | 0.77 | 0.91 |
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+ | endothelial cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 0.50 |
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90
  </details>
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