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tabula_sapiens_Trachea

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biology
genomics
single-cell
anndata_version:0.11.1
tissue: Trachea
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@@ -31,31 +31,31 @@ 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
- | basal cell | 1038 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.90 | 0.97 | 0.97 | 0.99 |
35
- | neutrophil | 479 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.94 | 0.99 | 0.99 | 0.99 |
36
- | fibroblast | 174 | 0.98 | 0.96 | 0.97 | 0.99 | 0.00 | 0.92 | 0.97 | 0.98 | 0.98 |
37
- | CD8-positive, alpha-beta T cell | 124 | 0.92 | 0.92 | 0.94 | 0.84 | 0.00 | 0.95 | 0.95 | 0.93 | 0.95 |
38
- | ciliated columnar cell of tracheobronchial tree | 63 | 0.95 | 0.92 | 0.93 | 0.98 | 0.00 | 0.77 | 0.92 | 0.92 | 0.94 |
39
- | macrophage | 68 | 0.96 | 0.96 | 0.96 | 0.94 | 0.00 | 0.93 | 0.98 | 0.93 | 0.98 |
40
- | B cell | 62 | 0.96 | 0.96 | 0.98 | 0.97 | 0.00 | 0.98 | 1.00 | 1.00 | 0.98 |
41
- | endothelial cell | 53 | 0.97 | 0.97 | 0.99 | 0.99 | 0.00 | 0.94 | 1.00 | 1.00 | 1.00 |
42
- | serous cell of epithelium of trachea | 26 | 0.48 | 0.27 | 0.70 | 0.69 | 0.00 | 0.36 | 0.51 | 0.56 | 0.71 |
43
- | plasma cell | 20 | 0.95 | 0.93 | 0.98 | 1.00 | 0.00 | 0.93 | 0.93 | 0.95 | 0.98 |
44
- | CD4-positive, alpha-beta T cell | 29 | 0.79 | 0.72 | 0.77 | 0.20 | 0.00 | 0.79 | 0.86 | 0.83 | 0.85 |
45
- | mucus secreting cell | 31 | 0.72 | 0.80 | 0.83 | 0.83 | 0.00 | 0.71 | 0.77 | 0.82 | 0.86 |
46
- | tracheal goblet cell | 32 | 0.74 | 0.65 | 0.86 | 0.89 | 0.00 | 0.74 | 0.84 | 0.79 | 0.92 |
47
- | connective tissue cell | 8 | 0.94 | 0.00 | 0.89 | 1.00 | 0.00 | 0.80 | 0.94 | 0.94 | 1.00 |
48
- | smooth muscle cell | 17 | 0.84 | 0.79 | 0.89 | 0.91 | 0.00 | 0.85 | 0.84 | 0.91 | 0.84 |
49
- | mast cell | 13 | 0.96 | 0.96 | 0.96 | 0.96 | 0.00 | 0.96 | 1.00 | 1.00 | 0.96 |
50
- | monocyte | 7 | 0.80 | 0.77 | 0.67 | 0.67 | 0.00 | 0.57 | 0.82 | 0.77 | 0.80 |
51
- | natural killer cell | 7 | 0.58 | 0.71 | 0.73 | 0.53 | 0.00 | 0.74 | 0.82 | 0.78 | 0.82 |
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- | granulocyte | 4 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 0.11 | 0.00 | 0.29 | 0.00 |
53
- | mature NK T cell | 5 | 0.29 | 0.00 | 0.67 | 0.33 | 0.00 | 0.75 | 0.91 | 1.00 | 1.00 |
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- | T cell | 2 | 0.00 | 0.67 | 1.00 | 0.00 | 0.00 | 0.12 | 0.00 | 0.00 | 0.00 |
55
- | ionocyte | 2 | 0.80 | 0.00 | 0.50 | 0.67 | 0.00 | 0.20 | 1.00 | 1.00 | 1.00 |
56
- | regulatory T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
57
- | intermediate monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
58
- | non-classical monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
59
  | innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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  | plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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  | myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
@@ -64,33 +64,33 @@ The train accuracies are computed on the training data.
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65
  | Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
66
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
67
- | basal cell | 9209 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.94 | 0.98 | 0.98 | 0.99 |
68
- | neutrophil | 4205 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.96 | 0.99 | 0.99 | 1.00 |
69
- | fibroblast | 1626 | 0.96 | 0.93 | 0.97 | 0.98 | 0.00 | 0.94 | 0.98 | 0.99 | 0.98 |
70
- | CD8-positive, alpha-beta T cell | 1078 | 0.89 | 0.91 | 0.94 | 0.88 | 0.00 | 0.95 | 0.97 | 0.98 | 0.96 |
71
- | ciliated columnar cell of tracheobronchial tree | 650 | 0.96 | 0.97 | 0.96 | 0.98 | 0.00 | 0.87 | 0.98 | 0.97 | 0.99 |
72
- | macrophage | 644 | 0.92 | 0.92 | 0.94 | 0.92 | 0.00 | 0.95 | 0.98 | 0.99 | 0.96 |
73
- | B cell | 565 | 0.97 | 0.96 | 0.97 | 0.97 | 0.00 | 0.98 | 1.00 | 1.00 | 0.99 |
74
- | endothelial cell | 533 | 0.96 | 0.97 | 0.98 | 0.99 | 0.00 | 0.94 | 0.99 | 0.98 | 0.99 |
75
- | serous cell of epithelium of trachea | 300 | 0.67 | 0.02 | 0.88 | 0.88 | 0.00 | 0.67 | 0.78 | 0.80 | 0.92 |
76
- | plasma cell | 272 | 0.98 | 0.97 | 0.99 | 0.96 | 0.00 | 0.98 | 1.00 | 0.99 | 0.99 |
77
- | CD4-positive, alpha-beta T cell | 249 | 0.72 | 0.67 | 0.78 | 0.44 | 0.00 | 0.86 | 0.94 | 0.96 | 0.85 |
78
- | mucus secreting cell | 239 | 0.71 | 0.73 | 0.87 | 0.88 | 0.00 | 0.75 | 0.87 | 0.90 | 0.92 |
79
- | tracheal goblet cell | 200 | 0.73 | 0.50 | 0.88 | 0.88 | 0.00 | 0.79 | 0.86 | 0.82 | 0.96 |
80
- | connective tissue cell | 144 | 0.81 | 0.00 | 0.90 | 0.96 | 0.00 | 0.96 | 0.97 | 0.97 | 0.98 |
81
- | smooth muscle cell | 114 | 0.79 | 0.74 | 0.86 | 0.90 | 0.00 | 0.80 | 0.91 | 0.90 | 0.88 |
82
- | mast cell | 106 | 0.96 | 0.96 | 0.96 | 0.99 | 0.00 | 0.95 | 1.00 | 1.00 | 1.00 |
83
- | monocyte | 74 | 0.57 | 0.48 | 0.73 | 0.50 | 0.00 | 0.76 | 0.95 | 0.99 | 0.82 |
84
- | natural killer cell | 57 | 0.53 | 0.47 | 0.67 | 0.55 | 0.00 | 0.81 | 0.84 | 0.83 | 0.89 |
85
- | granulocyte | 35 | 0.00 | 0.00 | 0.36 | 0.36 | 0.00 | 0.17 | 0.72 | 0.69 | 0.48 |
86
- | mature NK T cell | 32 | 0.31 | 0.06 | 0.67 | 0.39 | 0.00 | 0.69 | 0.91 | 0.94 | 0.84 |
87
- | T cell | 17 | 0.00 | 0.00 | 0.48 | 0.00 | 0.00 | 0.27 | 1.00 | 0.92 | 0.87 |
88
- | ionocyte | 16 | 0.42 | 0.00 | 0.83 | 0.69 | 0.00 | 0.43 | 1.00 | 0.89 | 1.00 |
89
- | regulatory T cell | 14 | 0.00 | 0.00 | 0.32 | 0.24 | 0.00 | 0.43 | 1.00 | 1.00 | 0.67 |
90
- | intermediate monocyte | 16 | 0.00 | 0.00 | 0.47 | 0.23 | 0.00 | 0.67 | 0.97 | 0.97 | 0.81 |
91
- | non-classical monocyte | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.75 | 1.00 | 1.00 | 0.00 |
92
- | innate lymphoid cell | 2 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.67 | 0.80 | 1.00 | 1.00 |
93
- | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.33 | 1.00 | 1.00 | 1.00 |
94
  | myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
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  </details>
 
31
 
32
  | Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
33
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
34
+ | basal cell | 1021 | 0.99 | 0.98 | 0.98 | 0.99 | 0.00 | 0.89 | 0.98 | 0.97 | 0.99 |
35
+ | neutrophil | 461 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.92 | 0.99 | 0.99 | 0.99 |
36
+ | fibroblast | 169 | 0.96 | 0.95 | 0.97 | 0.96 | 0.00 | 0.95 | 0.97 | 0.96 | 0.97 |
37
+ | CD8-positive, alpha-beta T cell | 126 | 0.90 | 0.93 | 0.92 | 0.87 | 0.00 | 0.95 | 0.92 | 0.95 | 0.94 |
38
+ | ciliated columnar cell of tracheobronchial tree | 69 | 0.97 | 0.97 | 0.95 | 0.98 | 0.00 | 0.82 | 0.96 | 0.96 | 0.96 |
39
+ | macrophage | 73 | 0.95 | 0.97 | 0.97 | 0.95 | 0.00 | 0.92 | 0.97 | 0.97 | 0.98 |
40
+ | B cell | 66 | 0.96 | 0.97 | 0.99 | 0.97 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |
41
+ | endothelial cell | 54 | 0.96 | 0.95 | 0.96 | 0.97 | 0.00 | 0.95 | 0.97 | 0.97 | 0.97 |
42
+ | serous cell of epithelium of trachea | 24 | 0.62 | 0.15 | 0.71 | 0.72 | 0.00 | 0.28 | 0.48 | 0.48 | 0.74 |
43
+ | plasma cell | 28 | 0.95 | 0.95 | 0.95 | 0.96 | 0.00 | 0.95 | 0.95 | 0.95 | 0.95 |
44
+ | CD4-positive, alpha-beta T cell | 33 | 0.78 | 0.78 | 0.78 | 0.69 | 0.00 | 0.82 | 0.82 | 0.93 | 0.89 |
45
+ | mucus secreting cell | 34 | 0.85 | 0.83 | 0.87 | 0.85 | 0.00 | 0.78 | 0.77 | 0.78 | 0.86 |
46
+ | tracheal goblet cell | 34 | 0.87 | 0.70 | 0.91 | 0.88 | 0.00 | 0.70 | 0.90 | 0.88 | 0.91 |
47
+ | connective tissue cell | 10 | 0.86 | 0.00 | 0.95 | 0.46 | 0.00 | 0.87 | 0.91 | 0.82 | 0.95 |
48
+ | smooth muscle cell | 17 | 0.78 | 0.80 | 0.86 | 0.91 | 0.00 | 0.60 | 0.82 | 0.82 | 0.82 |
49
+ | mast cell | 17 | 0.94 | 0.94 | 0.97 | 0.97 | 0.00 | 0.94 | 0.94 | 0.97 | 0.94 |
50
+ | monocyte | 6 | 0.77 | 0.91 | 0.91 | 0.67 | 0.00 | 0.71 | 1.00 | 0.83 | 0.91 |
51
+ | natural killer cell | 9 | 0.62 | 0.78 | 0.80 | 0.00 | 0.00 | 0.76 | 0.74 | 0.80 | 0.70 |
52
+ | granulocyte | 5 | 0.00 | 0.00 | 0.33 | 0.00 | 0.00 | 0.12 | 0.47 | 0.36 | 0.33 |
53
+ | mature NK T cell | 5 | 0.22 | 0.00 | 0.50 | 0.00 | 0.00 | 0.50 | 0.67 | 0.80 | 0.44 |
54
+ | T cell | 2 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
55
+ | ionocyte | 1 | 0.67 | 0.00 | 0.67 | 0.67 | 0.00 | 0.07 | 0.67 | 1.00 | 0.67 |
56
+ | regulatory T cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 |
57
+ | intermediate monocyte | 1 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
58
+ | non-classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
59
  | innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
60
  | plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
61
  | myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
 
64
 
65
  | Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
66
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
67
+ | basal cell | 9226 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.91 | 0.98 | 0.97 | 0.99 |
68
+ | neutrophil | 4223 | 0.99 | 0.99 | 0.98 | 0.99 | 0.00 | 0.95 | 0.99 | 0.99 | 1.00 |
69
+ | fibroblast | 1631 | 0.97 | 0.93 | 0.98 | 0.98 | 0.00 | 0.96 | 0.98 | 0.98 | 0.99 |
70
+ | CD8-positive, alpha-beta T cell | 1076 | 0.88 | 0.91 | 0.94 | 0.90 | 0.00 | 0.95 | 0.98 | 0.99 | 0.96 |
71
+ | ciliated columnar cell of tracheobronchial tree | 644 | 0.97 | 0.97 | 0.97 | 0.98 | 0.00 | 0.87 | 0.99 | 0.97 | 0.99 |
72
+ | macrophage | 639 | 0.92 | 0.93 | 0.94 | 0.93 | 0.00 | 0.94 | 0.98 | 0.99 | 0.97 |
73
+ | B cell | 561 | 0.96 | 0.96 | 0.97 | 0.97 | 0.00 | 0.98 | 1.00 | 0.99 | 0.99 |
74
+ | endothelial cell | 532 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.96 | 0.99 | 0.99 | 0.99 |
75
+ | serous cell of epithelium of trachea | 302 | 0.79 | 0.01 | 0.87 | 0.83 | 0.00 | 0.51 | 0.79 | 0.70 | 0.93 |
76
+ | plasma cell | 264 | 0.97 | 0.97 | 0.99 | 0.98 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
77
+ | CD4-positive, alpha-beta T cell | 245 | 0.64 | 0.64 | 0.78 | 0.66 | 0.00 | 0.88 | 0.95 | 0.97 | 0.86 |
78
+ | mucus secreting cell | 236 | 0.77 | 0.67 | 0.86 | 0.85 | 0.00 | 0.78 | 0.85 | 0.82 | 0.91 |
79
+ | tracheal goblet cell | 198 | 0.81 | 0.51 | 0.90 | 0.91 | 0.00 | 0.60 | 0.91 | 0.86 | 0.96 |
80
+ | connective tissue cell | 142 | 0.80 | 0.00 | 0.91 | 0.95 | 0.00 | 0.90 | 0.93 | 0.90 | 0.98 |
81
+ | smooth muscle cell | 114 | 0.78 | 0.81 | 0.88 | 0.91 | 0.00 | 0.57 | 0.91 | 0.91 | 0.88 |
82
+ | mast cell | 102 | 0.97 | 0.97 | 0.97 | 0.99 | 0.00 | 0.96 | 1.00 | 1.00 | 1.00 |
83
+ | monocyte | 75 | 0.60 | 0.62 | 0.74 | 0.58 | 0.00 | 0.79 | 0.95 | 0.97 | 0.88 |
84
+ | natural killer cell | 55 | 0.63 | 0.60 | 0.72 | 0.35 | 0.00 | 0.79 | 0.92 | 0.90 | 0.93 |
85
+ | granulocyte | 34 | 0.00 | 0.00 | 0.20 | 0.16 | 0.00 | 0.14 | 0.60 | 0.63 | 0.29 |
86
+ | mature NK T cell | 32 | 0.28 | 0.06 | 0.69 | 0.44 | 0.00 | 0.65 | 0.93 | 0.98 | 0.92 |
87
+ | T cell | 17 | 0.00 | 0.00 | 0.64 | 0.29 | 0.00 | 0.67 | 1.00 | 1.00 | 0.94 |
88
+ | ionocyte | 17 | 0.78 | 0.00 | 0.88 | 0.94 | 0.00 | 0.13 | 1.00 | 1.00 | 0.94 |
89
+ | regulatory T cell | 14 | 0.00 | 0.00 | 0.24 | 0.00 | 0.00 | 0.84 | 1.00 | 1.00 | 0.60 |
90
+ | intermediate monocyte | 15 | 0.00 | 0.00 | 0.42 | 0.38 | 0.00 | 0.81 | 0.94 | 1.00 | 0.85 |
91
+ | non-classical monocyte | 5 | 0.00 | 0.00 | 0.33 | 0.57 | 0.00 | 0.67 | 0.91 | 1.00 | 0.75 |
92
+ | innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 0.80 | 1.00 |
93
+ | plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |
94
  | myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
95
 
96
  </details>