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tabula_sapiens_Lymph_Node

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biology
genomics
single-cell
anndata_version:0.11.1
tissue: Lymph_Node
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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
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
34
- | B cell | 5482 | 0.99 | 0.99 | 0.99 | 1.00 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |
35
- | CD4-positive, alpha-beta T cell | 3919 | 0.76 | 0.86 | 0.86 | 0.85 | 0.00 | 0.70 | 0.63 | 0.77 | 0.87 |
36
- | CD8-positive, alpha-beta T cell | 1472 | 0.79 | 0.81 | 0.80 | 0.74 | 0.00 | 0.79 | 0.77 | 0.84 | 0.83 |
37
- | plasma cell | 608 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.97 | 0.98 | 0.99 |
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- | naive thymus-derived CD4-positive, alpha-beta T cell | 404 | 0.19 | 0.02 | 0.08 | 0.07 | 0.00 | 0.28 | 0.41 | 0.52 | 0.28 |
39
- | macrophage | 166 | 0.92 | 0.93 | 0.91 | 0.89 | 0.00 | 0.86 | 0.84 | 0.91 | 0.92 |
40
- | natural killer cell | 175 | 0.57 | 0.64 | 0.64 | 0.60 | 0.00 | 0.65 | 0.55 | 0.64 | 0.65 |
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- | T cell | 123 | 0.69 | 0.72 | 0.65 | 0.58 | 0.00 | 0.43 | 0.45 | 0.64 | 0.69 |
42
- | mature NK T cell | 120 | 0.49 | 0.43 | 0.46 | 0.48 | 0.00 | 0.41 | 0.45 | 0.55 | 0.54 |
43
- | regulatory T cell | 92 | 0.17 | 0.02 | 0.09 | 0.06 | 0.00 | 0.22 | 0.18 | 0.22 | 0.31 |
44
- | monocyte | 68 | 0.76 | 0.76 | 0.77 | 0.75 | 0.00 | 0.67 | 0.75 | 0.80 | 0.85 |
45
- | innate lymphoid cell | 86 | 0.54 | 0.52 | 0.41 | 0.29 | 0.00 | 0.54 | 0.43 | 0.64 | 0.69 |
46
- | classical monocyte | 52 | 0.68 | 0.76 | 0.67 | 0.59 | 0.00 | 0.65 | 0.74 | 0.79 | 0.78 |
47
- | neutrophil | 24 | 0.87 | 0.92 | 0.96 | 0.96 | 0.00 | 0.87 | 0.96 | 0.94 | 0.94 |
48
- | intermediate monocyte | 22 | 0.00 | 0.46 | 0.36 | 0.35 | 0.00 | 0.42 | 0.69 | 0.78 | 0.60 |
49
- | mast cell | 19 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.95 | 0.97 | 1.00 | 1.00 |
50
- | endothelial cell | 24 | 0.72 | 0.71 | 0.74 | 0.68 | 0.00 | 0.69 | 0.81 | 0.86 | 0.82 |
51
- | myeloid dendritic cell | 13 | 0.67 | 0.67 | 0.43 | 0.45 | 0.00 | 0.33 | 0.61 | 0.71 | 0.67 |
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- | CD4-positive, alpha-beta thymocyte | 9 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.27 | 0.15 | 0.35 | 0.36 |
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- | stromal cell | 13 | 0.81 | 0.53 | 0.77 | 0.74 | 0.00 | 0.84 | 0.96 | 0.88 | 0.93 |
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- | non-classical monocyte | 7 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.27 | 0.00 | 0.43 | 0.00 |
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- | CD8-positive, alpha-beta thymocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.21 | 0.24 | 0.17 | 0.00 |
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- | erythrocyte | 2 | 0.33 | 0.40 | 0.22 | 1.00 | 0.00 | 0.24 | 1.00 | 1.00 | 0.80 |
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- | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.04 | 0.00 | 0.00 | 0.00 |
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- | hematopoietic precursor cell | 3 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.10 | 0.00 | 0.00 | 0.00 |
59
 
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
- | B cell | 49264 | 0.99 | 0.98 | 1.00 | 1.00 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |
65
- | CD4-positive, alpha-beta T cell | 35361 | 0.76 | 0.86 | 0.89 | 0.88 | 0.00 | 0.73 | 0.63 | 0.78 | 0.88 |
66
- | CD8-positive, alpha-beta T cell | 13210 | 0.79 | 0.82 | 0.85 | 0.81 | 0.00 | 0.80 | 0.78 | 0.86 | 0.85 |
67
- | plasma cell | 5336 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.99 | 0.99 |
68
- | naive thymus-derived CD4-positive, alpha-beta T cell | 3750 | 0.20 | 0.01 | 0.20 | 0.14 | 0.00 | 0.32 | 0.42 | 0.55 | 0.33 |
69
- | macrophage | 1628 | 0.90 | 0.91 | 0.92 | 0.92 | 0.00 | 0.91 | 0.91 | 0.94 | 0.94 |
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- | natural killer cell | 1404 | 0.57 | 0.67 | 0.76 | 0.74 | 0.00 | 0.72 | 0.64 | 0.73 | 0.81 |
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- | T cell | 1158 | 0.69 | 0.68 | 0.73 | 0.71 | 0.00 | 0.44 | 0.48 | 0.67 | 0.71 |
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- | mature NK T cell | 904 | 0.48 | 0.41 | 0.63 | 0.59 | 0.00 | 0.54 | 0.56 | 0.70 | 0.74 |
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- | regulatory T cell | 876 | 0.18 | 0.02 | 0.32 | 0.22 | 0.00 | 0.27 | 0.22 | 0.25 | 0.38 |
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- | monocyte | 698 | 0.77 | 0.79 | 0.82 | 0.86 | 0.00 | 0.77 | 0.84 | 0.90 | 0.94 |
75
- | innate lymphoid cell | 659 | 0.46 | 0.53 | 0.54 | 0.52 | 0.00 | 0.70 | 0.49 | 0.67 | 0.75 |
76
- | classical monocyte | 500 | 0.63 | 0.67 | 0.74 | 0.69 | 0.00 | 0.81 | 0.89 | 0.92 | 0.87 |
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- | neutrophil | 279 | 0.86 | 0.93 | 0.98 | 0.96 | 0.00 | 0.88 | 0.99 | 0.97 | 0.95 |
78
- | intermediate monocyte | 259 | 0.00 | 0.49 | 0.63 | 0.54 | 0.00 | 0.77 | 0.89 | 0.94 | 0.85 |
79
- | mast cell | 193 | 0.96 | 0.97 | 0.97 | 0.97 | 0.00 | 0.90 | 0.98 | 0.98 | 0.97 |
80
- | endothelial cell | 172 | 0.68 | 0.67 | 0.78 | 0.77 | 0.00 | 0.74 | 0.94 | 0.96 | 0.90 |
81
- | myeloid dendritic cell | 109 | 0.49 | 0.51 | 0.62 | 0.48 | 0.00 | 0.31 | 0.89 | 0.88 | 0.88 |
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- | CD4-positive, alpha-beta thymocyte | 113 | 0.00 | 0.00 | 0.02 | 0.28 | 0.00 | 0.45 | 0.45 | 0.74 | 0.66 |
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- | stromal cell | 98 | 0.85 | 0.42 | 0.83 | 0.88 | 0.00 | 0.81 | 0.98 | 0.98 | 0.98 |
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- | non-classical monocyte | 64 | 0.00 | 0.00 | 0.19 | 0.14 | 0.00 | 0.42 | 0.76 | 0.93 | 0.60 |
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- | CD8-positive, alpha-beta thymocyte | 56 | 0.00 | 0.00 | 0.16 | 0.19 | 0.00 | 0.43 | 0.49 | 0.67 | 0.59 |
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- | erythrocyte | 40 | 0.68 | 0.83 | 0.62 | 0.88 | 0.00 | 0.30 | 0.98 | 0.90 | 0.94 |
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- | plasmacytoid dendritic cell | 15 | 0.00 | 0.64 | 0.81 | 0.54 | 0.00 | 0.06 | 1.00 | 1.00 | 1.00 |
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- | hematopoietic precursor cell | 9 | 0.00 | 0.00 | 0.63 | 0.53 | 0.00 | 0.13 | 1.00 | 1.00 | 0.94 |
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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
+ | B cell | 5434 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
35
+ | CD4-positive, alpha-beta T cell | 3941 | 0.75 | 0.87 | 0.87 | 0.86 | 0.00 | 0.50 | 0.62 | 0.79 | 0.86 |
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+ | CD8-positive, alpha-beta T cell | 1464 | 0.77 | 0.81 | 0.81 | 0.78 | 0.00 | 0.79 | 0.77 | 0.85 | 0.83 |
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+ | plasma cell | 596 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
38
+ | naive thymus-derived CD4-positive, alpha-beta T cell | 436 | 0.22 | 0.03 | 0.06 | 0.04 | 0.00 | 0.25 | 0.38 | 0.55 | 0.31 |
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+ | macrophage | 171 | 0.90 | 0.93 | 0.91 | 0.91 | 0.00 | 0.90 | 0.86 | 0.91 | 0.93 |
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+ | natural killer cell | 177 | 0.63 | 0.73 | 0.70 | 0.65 | 0.00 | 0.68 | 0.58 | 0.66 | 0.70 |
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+ | T cell | 127 | 0.62 | 0.80 | 0.73 | 0.72 | 0.00 | 0.55 | 0.51 | 0.67 | 0.70 |
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+ | mature NK T cell | 115 | 0.55 | 0.44 | 0.50 | 0.43 | 0.00 | 0.36 | 0.44 | 0.53 | 0.53 |
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+ | regulatory T cell | 102 | 0.23 | 0.02 | 0.21 | 0.15 | 0.00 | 0.19 | 0.20 | 0.25 | 0.36 |
44
+ | monocyte | 73 | 0.78 | 0.81 | 0.78 | 0.79 | 0.00 | 0.71 | 0.84 | 0.81 | 0.84 |
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+ | innate lymphoid cell | 81 | 0.61 | 0.63 | 0.51 | 0.44 | 0.00 | 0.46 | 0.46 | 0.57 | 0.61 |
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+ | classical monocyte | 52 | 0.60 | 0.73 | 0.65 | 0.64 | 0.00 | 0.67 | 0.75 | 0.87 | 0.83 |
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+ | neutrophil | 28 | 0.90 | 0.96 | 0.96 | 0.95 | 0.00 | 0.93 | 0.96 | 0.91 | 0.95 |
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+ | intermediate monocyte | 24 | 0.00 | 0.51 | 0.53 | 0.52 | 0.00 | 0.65 | 0.69 | 0.83 | 0.85 |
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+ | mast cell | 15 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |
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+ | endothelial cell | 21 | 0.67 | 0.68 | 0.62 | 0.62 | 0.00 | 0.62 | 0.76 | 0.72 | 0.77 |
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+ | myeloid dendritic cell | 14 | 0.62 | 0.67 | 0.43 | 0.52 | 0.00 | 0.54 | 0.80 | 0.65 | 0.76 |
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+ | CD4-positive, alpha-beta thymocyte | 10 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.17 | 0.10 | 0.17 | 0.00 |
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+ | stromal cell | 11 | 0.82 | 0.80 | 0.85 | 0.83 | 0.00 | 0.87 | 0.92 | 0.87 | 0.92 |
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+ | non-classical monocyte | 4 | 0.15 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.27 | 0.50 | 0.40 |
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+ | CD8-positive, alpha-beta thymocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.16 | 0.33 | 0.20 | 0.00 |
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+ | erythrocyte | 2 | 0.80 | 0.80 | 0.50 | 1.00 | 0.00 | 0.36 | 1.00 | 0.80 | 1.00 |
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+ | plasmacytoid dendritic cell | 2 | 0.00 | 0.00 | 0.67 | 0.50 | 0.00 | 0.18 | 0.67 | 0.00 | 0.67 |
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+ | hematopoietic precursor cell | 4 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.25 | 0.40 | 0.00 | 0.00 |
59
 
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
+ | B cell | 49312 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
65
+ | CD4-positive, alpha-beta T cell | 35339 | 0.75 | 0.88 | 0.89 | 0.88 | 0.00 | 0.49 | 0.64 | 0.79 | 0.88 |
66
+ | CD8-positive, alpha-beta T cell | 13218 | 0.78 | 0.82 | 0.86 | 0.82 | 0.00 | 0.80 | 0.78 | 0.86 | 0.85 |
67
+ | plasma cell | 5348 | 0.98 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
68
+ | naive thymus-derived CD4-positive, alpha-beta T cell | 3718 | 0.20 | 0.02 | 0.20 | 0.16 | 0.00 | 0.24 | 0.39 | 0.55 | 0.37 |
69
+ | macrophage | 1623 | 0.90 | 0.92 | 0.93 | 0.93 | 0.00 | 0.91 | 0.92 | 0.95 | 0.95 |
70
+ | natural killer cell | 1402 | 0.62 | 0.73 | 0.80 | 0.78 | 0.00 | 0.76 | 0.70 | 0.76 | 0.83 |
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+ | T cell | 1154 | 0.60 | 0.73 | 0.78 | 0.74 | 0.00 | 0.58 | 0.52 | 0.69 | 0.70 |
72
+ | mature NK T cell | 909 | 0.54 | 0.47 | 0.64 | 0.65 | 0.00 | 0.60 | 0.63 | 0.69 | 0.75 |
73
+ | regulatory T cell | 866 | 0.21 | 0.02 | 0.40 | 0.29 | 0.00 | 0.20 | 0.22 | 0.27 | 0.39 |
74
+ | monocyte | 693 | 0.80 | 0.79 | 0.85 | 0.88 | 0.00 | 0.85 | 0.87 | 0.92 | 0.94 |
75
+ | innate lymphoid cell | 664 | 0.57 | 0.64 | 0.61 | 0.54 | 0.00 | 0.74 | 0.54 | 0.63 | 0.74 |
76
+ | classical monocyte | 500 | 0.60 | 0.67 | 0.72 | 0.74 | 0.00 | 0.78 | 0.90 | 0.93 | 0.88 |
77
+ | neutrophil | 275 | 0.85 | 0.96 | 0.97 | 1.00 | 0.00 | 0.98 | 0.99 | 0.97 | 0.97 |
78
+ | intermediate monocyte | 257 | 0.00 | 0.52 | 0.61 | 0.60 | 0.00 | 0.78 | 0.88 | 0.92 | 0.89 |
79
+ | mast cell | 197 | 0.97 | 0.97 | 0.97 | 0.97 | 0.00 | 0.96 | 0.98 | 0.98 | 0.97 |
80
+ | endothelial cell | 175 | 0.68 | 0.61 | 0.78 | 0.80 | 0.00 | 0.79 | 0.94 | 0.95 | 0.89 |
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+ | myeloid dendritic cell | 108 | 0.50 | 0.56 | 0.61 | 0.63 | 0.00 | 0.41 | 0.92 | 0.86 | 0.85 |
82
+ | CD4-positive, alpha-beta thymocyte | 112 | 0.00 | 0.00 | 0.07 | 0.21 | 0.00 | 0.45 | 0.51 | 0.68 | 0.59 |
83
+ | stromal cell | 100 | 0.84 | 0.46 | 0.84 | 0.92 | 0.00 | 0.89 | 0.99 | 0.97 | 0.95 |
84
+ | non-classical monocyte | 67 | 0.26 | 0.16 | 0.27 | 0.17 | 0.00 | 0.33 | 0.76 | 0.77 | 0.68 |
85
+ | CD8-positive, alpha-beta thymocyte | 56 | 0.00 | 0.00 | 0.03 | 0.18 | 0.00 | 0.39 | 0.77 | 0.68 | 0.63 |
86
+ | erythrocyte | 40 | 0.70 | 0.74 | 0.65 | 0.84 | 0.00 | 0.39 | 0.96 | 0.92 | 0.90 |
87
+ | plasmacytoid dendritic cell | 14 | 0.00 | 0.60 | 0.83 | 0.75 | 0.00 | 0.16 | 0.97 | 0.97 | 1.00 |
88
+ | hematopoietic precursor cell | 8 | 0.00 | 0.00 | 0.62 | 0.29 | 0.00 | 0.36 | 1.00 | 1.00 | 0.86 |
89
 
90
  </details>
91