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tabula_sapiens_Lymph_Node

Joblib
popV
biology
genomics
single-cell
anndata_version:0.11.3
python_version:3.11.11
tissue: Lymph_Node
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@@ -32,61 +32,61 @@ 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 bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
34
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
35
- | B cell | 5491 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |
36
- | CD4-positive, alpha-beta T cell | 3913 | 0.79 | 0.87 | 0.86 | 0.85 | 0.00 | 0.63 | 0.63 | 0.78 | 0.87 |
37
- | CD8-positive, alpha-beta T cell | 1463 | 0.79 | 0.81 | 0.80 | 0.75 | 0.00 | 0.70 | 0.75 | 0.85 | 0.83 |
38
- | plasma cell | 601 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
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- | naive thymus-derived CD4-positive, alpha-beta T cell | 413 | 0.15 | 0.02 | 0.04 | 0.07 | 0.00 | 0.33 | 0.38 | 0.54 | 0.23 |
40
- | macrophage | 165 | 0.92 | 0.91 | 0.91 | 0.90 | 0.00 | 0.87 | 0.87 | 0.90 | 0.92 |
41
- | natural killer cell | 182 | 0.65 | 0.73 | 0.69 | 0.62 | 0.00 | 0.60 | 0.55 | 0.66 | 0.67 |
42
- | T cell | 122 | 0.62 | 0.73 | 0.67 | 0.64 | 0.00 | 0.45 | 0.45 | 0.60 | 0.69 |
43
- | mature NK T cell | 119 | 0.50 | 0.48 | 0.51 | 0.44 | 0.00 | 0.46 | 0.44 | 0.55 | 0.53 |
44
- | regulatory T cell | 97 | 0.25 | 0.02 | 0.21 | 0.10 | 0.00 | 0.21 | 0.19 | 0.24 | 0.34 |
45
- | monocyte | 67 | 0.79 | 0.79 | 0.75 | 0.73 | 0.00 | 0.65 | 0.78 | 0.86 | 0.86 |
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- | innate lymphoid cell | 86 | 0.64 | 0.66 | 0.51 | 0.39 | 0.00 | 0.54 | 0.53 | 0.62 | 0.68 |
47
- | classical monocyte | 52 | 0.72 | 0.73 | 0.65 | 0.53 | 0.00 | 0.67 | 0.68 | 0.82 | 0.76 |
48
- | neutrophil | 25 | 1.00 | 0.98 | 0.98 | 0.91 | 0.00 | 0.67 | 0.96 | 0.96 | 0.96 |
49
- | intermediate monocyte | 22 | 0.52 | 0.47 | 0.38 | 0.22 | 0.00 | 0.55 | 0.65 | 0.88 | 0.68 |
50
- | mast cell | 18 | 1.00 | 1.00 | 0.94 | 1.00 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |
51
- | endothelial cell | 22 | 0.71 | 0.61 | 0.67 | 0.56 | 0.00 | 0.76 | 0.81 | 0.83 | 0.77 |
52
- | myeloid dendritic cell | 13 | 0.60 | 0.54 | 0.52 | 0.12 | 0.00 | 0.26 | 0.67 | 0.65 | 0.71 |
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- | CD4-positive, alpha-beta thymocyte | 9 | 0.00 | 0.00 | 0.00 | 0.18 | 0.00 | 0.22 | 0.10 | 0.21 | 0.20 |
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- | stromal cell | 12 | 0.83 | 0.87 | 0.74 | 0.81 | 0.00 | 0.92 | 0.92 | 0.96 | 0.92 |
55
- | non-classical monocyte | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.11 | 0.13 | 0.71 | 0.22 |
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- | CD8-positive, alpha-beta thymocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.09 | 0.29 | 0.57 | 0.00 |
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- | erythrocyte | 2 | 0.40 | 0.50 | 0.44 | 0.50 | 0.00 | 0.57 | 1.00 | 1.00 | 1.00 |
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- | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
59
- | hematopoietic precursor cell | 3 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 | 0.31 | 0.00 | 0.50 | 0.00 |
60
 
61
  The train accuracies are computed on the training data.
62
 
63
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
64
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
65
- | B cell | 49255 | 0.99 | 1.00 | 1.00 | 1.00 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |
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- | CD4-positive, alpha-beta T cell | 35367 | 0.79 | 0.88 | 0.89 | 0.88 | 0.00 | 0.61 | 0.64 | 0.78 | 0.88 |
67
- | CD8-positive, alpha-beta T cell | 13219 | 0.79 | 0.82 | 0.86 | 0.81 | 0.00 | 0.71 | 0.78 | 0.86 | 0.86 |
68
- | plasma cell | 5343 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
69
- | naive thymus-derived CD4-positive, alpha-beta T cell | 3741 | 0.18 | 0.02 | 0.18 | 0.18 | 0.00 | 0.33 | 0.40 | 0.55 | 0.32 |
70
- | macrophage | 1629 | 0.90 | 0.92 | 0.93 | 0.92 | 0.00 | 0.90 | 0.93 | 0.94 | 0.94 |
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- | natural killer cell | 1397 | 0.65 | 0.72 | 0.78 | 0.75 | 0.00 | 0.71 | 0.70 | 0.76 | 0.81 |
72
- | T cell | 1159 | 0.61 | 0.73 | 0.76 | 0.73 | 0.00 | 0.45 | 0.48 | 0.65 | 0.71 |
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- | mature NK T cell | 905 | 0.50 | 0.44 | 0.63 | 0.61 | 0.00 | 0.60 | 0.60 | 0.68 | 0.74 |
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- | regulatory T cell | 871 | 0.23 | 0.02 | 0.40 | 0.22 | 0.00 | 0.24 | 0.23 | 0.25 | 0.40 |
75
- | monocyte | 699 | 0.80 | 0.79 | 0.84 | 0.87 | 0.00 | 0.73 | 0.83 | 0.90 | 0.95 |
76
- | innate lymphoid cell | 659 | 0.57 | 0.65 | 0.60 | 0.60 | 0.00 | 0.73 | 0.57 | 0.66 | 0.73 |
77
- | classical monocyte | 500 | 0.64 | 0.67 | 0.74 | 0.68 | 0.00 | 0.80 | 0.88 | 0.90 | 0.87 |
78
- | neutrophil | 278 | 0.98 | 0.97 | 0.99 | 0.95 | 0.00 | 0.82 | 0.99 | 0.96 | 0.97 |
79
- | intermediate monocyte | 259 | 0.48 | 0.49 | 0.63 | 0.56 | 0.00 | 0.77 | 0.89 | 0.91 | 0.85 |
80
- | mast cell | 194 | 0.97 | 0.97 | 0.97 | 0.96 | 0.00 | 0.91 | 0.98 | 0.98 | 0.97 |
81
- | endothelial cell | 174 | 0.68 | 0.65 | 0.77 | 0.78 | 0.00 | 0.85 | 0.93 | 0.94 | 0.91 |
82
- | myeloid dendritic cell | 109 | 0.50 | 0.54 | 0.60 | 0.55 | 0.00 | 0.22 | 0.91 | 0.91 | 0.87 |
83
- | CD4-positive, alpha-beta thymocyte | 113 | 0.00 | 0.00 | 0.03 | 0.20 | 0.00 | 0.39 | 0.50 | 0.76 | 0.55 |
84
- | stromal cell | 99 | 0.84 | 0.45 | 0.82 | 0.88 | 0.00 | 0.88 | 0.98 | 0.99 | 0.97 |
85
- | non-classical monocyte | 65 | 0.00 | 0.09 | 0.26 | 0.09 | 0.00 | 0.63 | 0.82 | 0.79 | 0.75 |
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- | CD8-positive, alpha-beta thymocyte | 56 | 0.00 | 0.00 | 0.04 | 0.03 | 0.00 | 0.32 | 0.68 | 0.75 | 0.60 |
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- | erythrocyte | 40 | 0.84 | 0.79 | 0.69 | 0.85 | 0.00 | 0.73 | 0.96 | 0.86 | 0.93 |
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- | plasmacytoid dendritic cell | 15 | 0.00 | 0.64 | 0.81 | 0.74 | 0.00 | 0.27 | 1.00 | 1.00 | 1.00 |
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- | hematopoietic precursor cell | 9 | 0.00 | 0.00 | 0.53 | 0.35 | 0.00 | 0.33 | 0.95 | 0.90 | 0.75 |
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91
  </details>
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32
 
33
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
34
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
35
+ | B cell | 5485 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |
36
+ | CD4-positive, alpha-beta T cell | 3937 | 0.76 | 0.88 | 0.86 | 0.85 | 0.00 | 0.56 | 0.63 | 0.78 | 0.86 |
37
+ | CD8-positive, alpha-beta T cell | 1453 | 0.79 | 0.81 | 0.80 | 0.75 | 0.00 | 0.73 | 0.76 | 0.84 | 0.84 |
38
+ | plasma cell | 604 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |
39
+ | naive thymus-derived CD4-positive, alpha-beta T cell | 415 | 0.21 | 0.04 | 0.05 | 0.06 | 0.00 | 0.28 | 0.38 | 0.55 | 0.32 |
40
+ | macrophage | 162 | 0.91 | 0.91 | 0.89 | 0.88 | 0.00 | 0.85 | 0.86 | 0.89 | 0.92 |
41
+ | natural killer cell | 176 | 0.62 | 0.73 | 0.68 | 0.63 | 0.00 | 0.67 | 0.54 | 0.64 | 0.71 |
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+ | T cell | 121 | 0.62 | 0.76 | 0.68 | 0.64 | 0.00 | 0.57 | 0.47 | 0.63 | 0.67 |
43
+ | mature NK T cell | 116 | 0.48 | 0.46 | 0.50 | 0.47 | 0.00 | 0.48 | 0.48 | 0.55 | 0.58 |
44
+ | regulatory T cell | 93 | 0.23 | 0.00 | 0.09 | 0.07 | 0.00 | 0.15 | 0.19 | 0.23 | 0.34 |
45
+ | monocyte | 69 | 0.78 | 0.83 | 0.76 | 0.74 | 0.00 | 0.74 | 0.78 | 0.83 | 0.88 |
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+ | innate lymphoid cell | 85 | 0.61 | 0.65 | 0.48 | 0.40 | 0.00 | 0.49 | 0.55 | 0.64 | 0.65 |
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+ | classical monocyte | 52 | 0.69 | 0.74 | 0.66 | 0.59 | 0.00 | 0.74 | 0.68 | 0.81 | 0.78 |
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+ | neutrophil | 27 | 0.87 | 0.96 | 0.98 | 1.00 | 0.00 | 0.95 | 0.94 | 0.89 | 0.95 |
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+ | intermediate monocyte | 22 | 0.47 | 0.51 | 0.38 | 0.30 | 0.00 | 0.47 | 0.67 | 0.83 | 0.70 |
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+ | mast cell | 17 | 1.00 | 1.00 | 0.97 | 0.97 | 0.00 | 0.92 | 1.00 | 1.00 | 1.00 |
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+ | endothelial cell | 24 | 0.74 | 0.80 | 0.72 | 0.67 | 0.00 | 0.73 | 0.84 | 0.71 | 0.81 |
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+ | myeloid dendritic cell | 13 | 0.59 | 0.64 | 0.55 | 0.11 | 0.00 | 0.34 | 0.55 | 0.73 | 0.69 |
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+ | CD4-positive, alpha-beta thymocyte | 9 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.21 | 0.16 | 0.24 | 0.00 |
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+ | stromal cell | 12 | 0.80 | 0.70 | 0.74 | 0.64 | 0.00 | 0.75 | 0.88 | 0.88 | 0.89 |
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+ | non-classical monocyte | 6 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 | 0.07 | 0.31 | 0.92 | 0.25 |
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+ | CD8-positive, alpha-beta thymocyte | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.06 | 0.44 | 0.36 | 0.00 |
57
+ | erythrocyte | 2 | 0.40 | 0.50 | 0.29 | 0.67 | 0.00 | 0.36 | 0.80 | 1.00 | 1.00 |
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+ | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 |
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+ | hematopoietic precursor cell | 3 | 0.00 | 0.00 | 0.50 | 0.40 | 0.00 | 0.22 | 0.00 | 0.00 | 0.00 |
60
 
61
  The train accuracies are computed on the training data.
62
 
63
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
64
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
65
+ | B cell | 49261 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
66
+ | CD4-positive, alpha-beta T cell | 35343 | 0.74 | 0.88 | 0.89 | 0.88 | 0.00 | 0.59 | 0.63 | 0.79 | 0.87 |
67
+ | CD8-positive, alpha-beta T cell | 13229 | 0.78 | 0.82 | 0.86 | 0.81 | 0.00 | 0.75 | 0.78 | 0.86 | 0.85 |
68
+ | plasma cell | 5340 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
69
+ | naive thymus-derived CD4-positive, alpha-beta T cell | 3739 | 0.21 | 0.01 | 0.18 | 0.16 | 0.00 | 0.29 | 0.39 | 0.56 | 0.35 |
70
+ | macrophage | 1632 | 0.91 | 0.92 | 0.93 | 0.92 | 0.00 | 0.89 | 0.93 | 0.95 | 0.94 |
71
+ | natural killer cell | 1403 | 0.63 | 0.72 | 0.79 | 0.75 | 0.00 | 0.73 | 0.71 | 0.75 | 0.81 |
72
+ | T cell | 1160 | 0.62 | 0.72 | 0.77 | 0.73 | 0.00 | 0.59 | 0.48 | 0.67 | 0.69 |
73
+ | mature NK T cell | 908 | 0.50 | 0.44 | 0.64 | 0.63 | 0.00 | 0.59 | 0.60 | 0.68 | 0.73 |
74
+ | regulatory T cell | 875 | 0.22 | 0.01 | 0.39 | 0.25 | 0.00 | 0.19 | 0.23 | 0.26 | 0.39 |
75
+ | monocyte | 697 | 0.78 | 0.79 | 0.84 | 0.84 | 0.00 | 0.83 | 0.87 | 0.92 | 0.93 |
76
+ | innate lymphoid cell | 660 | 0.57 | 0.64 | 0.58 | 0.55 | 0.00 | 0.70 | 0.59 | 0.67 | 0.73 |
77
+ | classical monocyte | 500 | 0.58 | 0.67 | 0.72 | 0.69 | 0.00 | 0.82 | 0.86 | 0.91 | 0.86 |
78
+ | neutrophil | 276 | 0.86 | 0.96 | 0.99 | 0.96 | 0.00 | 0.96 | 1.00 | 0.97 | 0.97 |
79
+ | intermediate monocyte | 259 | 0.50 | 0.51 | 0.63 | 0.57 | 0.00 | 0.77 | 0.89 | 0.93 | 0.85 |
80
+ | mast cell | 195 | 0.97 | 0.97 | 0.96 | 0.96 | 0.00 | 0.92 | 0.98 | 0.98 | 0.97 |
81
+ | endothelial cell | 172 | 0.67 | 0.65 | 0.74 | 0.72 | 0.00 | 0.73 | 0.96 | 0.93 | 0.88 |
82
+ | myeloid dendritic cell | 109 | 0.50 | 0.52 | 0.62 | 0.50 | 0.00 | 0.29 | 0.90 | 0.95 | 0.87 |
83
+ | CD4-positive, alpha-beta thymocyte | 113 | 0.00 | 0.00 | 0.08 | 0.20 | 0.00 | 0.42 | 0.47 | 0.78 | 0.55 |
84
+ | stromal cell | 99 | 0.84 | 0.51 | 0.85 | 0.77 | 0.00 | 0.71 | 0.98 | 0.97 | 0.95 |
85
+ | non-classical monocyte | 65 | 0.00 | 0.06 | 0.26 | 0.14 | 0.00 | 0.39 | 0.74 | 0.84 | 0.57 |
86
+ | CD8-positive, alpha-beta thymocyte | 56 | 0.00 | 0.00 | 0.04 | 0.07 | 0.00 | 0.29 | 0.74 | 0.65 | 0.63 |
87
+ | erythrocyte | 40 | 0.82 | 0.82 | 0.67 | 0.84 | 0.00 | 0.51 | 0.92 | 0.93 | 0.95 |
88
+ | plasmacytoid dendritic cell | 15 | 0.00 | 0.70 | 0.81 | 0.81 | 0.00 | 0.23 | 0.97 | 0.97 | 0.97 |
89
+ | hematopoietic precursor cell | 9 | 0.00 | 0.00 | 0.59 | 0.38 | 0.00 | 0.44 | 0.95 | 0.95 | 0.89 |
90
 
91
  </details>
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