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tabula_sapiens_Large_Intestine

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popV
biology
genomics
single-cell
anndata_version:0.11.3
python_version:3.11.11
tissue: Large_Intestine
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@@ -32,67 +32,67 @@ 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
- | enterocyte of epithelium of large intestine | 471 | 0.82 | 0.84 | 0.84 | 0.82 | 0.00 | 0.79 | 0.82 | 0.86 | 0.84 |
36
- | CD4-positive, alpha-beta T cell | 413 | 0.85 | 0.88 | 0.86 | 0.72 | 0.00 | 0.73 | 0.86 | 0.86 | 0.89 |
37
- | plasma cell | 315 | 0.98 | 0.98 | 0.97 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
38
- | CD8-positive, alpha-beta T cell | 289 | 0.80 | 0.85 | 0.83 | 0.55 | 0.00 | 0.70 | 0.80 | 0.83 | 0.87 |
39
- | fibroblast | 250 | 0.96 | 0.98 | 0.98 | 0.97 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |
40
- | B cell | 228 | 0.99 | 0.99 | 0.99 | 0.98 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
41
- | gamma-delta T cell | 190 | 0.88 | 0.91 | 0.94 | 0.64 | 0.00 | 0.81 | 0.90 | 0.90 | 0.93 |
42
- | intestinal crypt stem cell of colon | 151 | 0.81 | 0.84 | 0.86 | 0.81 | 0.00 | 0.80 | 0.83 | 0.84 | 0.89 |
43
- | large intestine goblet cell | 169 | 0.90 | 0.94 | 0.93 | 0.79 | 0.00 | 0.79 | 0.91 | 0.90 | 0.93 |
44
- | enteroglial cell | 77 | 0.99 | 0.99 | 0.97 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |
45
- | regulatory T cell | 64 | 0.66 | 0.64 | 0.63 | 0.30 | 0.00 | 0.60 | 0.72 | 0.68 | 0.78 |
46
- | mast cell | 48 | 0.99 | 0.97 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
47
- | myeloid leukocyte | 31 | 0.89 | 0.91 | 0.92 | 0.85 | 0.00 | 0.98 | 0.92 | 0.95 | 1.00 |
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- | colon endothelial cell | 37 | 0.93 | 0.90 | 0.91 | 0.92 | 0.00 | 0.90 | 0.97 | 0.95 | 0.97 |
49
- | colon macrophage | 33 | 0.83 | 0.85 | 0.84 | 0.83 | 0.00 | 0.91 | 0.88 | 0.88 | 0.94 |
50
- | transit amplifying cell of colon | 25 | 0.75 | 0.59 | 0.67 | 0.60 | 0.00 | 0.55 | 0.60 | 0.64 | 0.77 |
51
- | naive thymus-derived CD4-positive, alpha-beta T cell | 23 | 0.75 | 0.75 | 0.69 | 0.12 | 0.00 | 0.77 | 0.69 | 0.72 | 0.83 |
52
- | paneth cell of colon | 21 | 0.63 | 0.37 | 0.68 | 0.76 | 0.00 | 0.64 | 0.73 | 0.52 | 0.85 |
53
- | tuft cell of colon | 17 | 1.00 | 1.00 | 0.97 | 0.94 | 0.00 | 0.89 | 1.00 | 0.97 | 1.00 |
54
- | myofibroblast cell | 11 | 0.79 | 0.88 | 0.87 | 0.95 | 0.00 | 0.79 | 0.96 | 0.83 | 0.88 |
55
- | monocyte | 4 | 0.86 | 0.86 | 0.55 | 0.67 | 0.00 | 0.86 | 0.86 | 0.75 | 0.86 |
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- | mature NK T cell | 6 | 0.00 | 0.29 | 0.29 | 0.00 | 0.00 | 0.32 | 0.50 | 0.60 | 0.44 |
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- | type L enteroendocrine cell | 5 | 0.59 | 0.83 | 0.77 | 0.75 | 0.00 | 0.48 | 1.00 | 0.91 | 1.00 |
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- | myeloid dendritic cell | 2 | 0.00 | 0.00 | 0.67 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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- | enterochromaffin-like cell | 6 | 0.00 | 0.80 | 0.67 | 0.67 | 0.00 | 0.67 | 0.91 | 1.00 | 1.00 |
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- | natural killer cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.67 | 0.67 | 0.00 |
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- | innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.67 | 0.50 | 0.00 |
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  | neutrophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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64
  The train accuracies are computed on the training data.
65
 
66
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
67
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
68
- | enterocyte of epithelium of large intestine | 4096 | 0.84 | 0.85 | 0.87 | 0.88 | 0.00 | 0.82 | 0.85 | 0.89 | 0.87 |
69
- | CD4-positive, alpha-beta T cell | 3827 | 0.86 | 0.88 | 0.91 | 0.80 | 0.00 | 0.80 | 0.89 | 0.90 | 0.92 |
70
- | plasma cell | 2993 | 0.98 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
71
- | CD8-positive, alpha-beta T cell | 2673 | 0.80 | 0.84 | 0.88 | 0.70 | 0.00 | 0.75 | 0.86 | 0.87 | 0.89 |
72
- | fibroblast | 2347 | 0.97 | 0.98 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
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- | B cell | 1841 | 0.99 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
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- | gamma-delta T cell | 1666 | 0.91 | 0.92 | 0.95 | 0.79 | 0.00 | 0.85 | 0.93 | 0.93 | 0.95 |
75
- | intestinal crypt stem cell of colon | 1581 | 0.85 | 0.86 | 0.91 | 0.88 | 0.00 | 0.85 | 0.89 | 0.91 | 0.93 |
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- | large intestine goblet cell | 1388 | 0.93 | 0.94 | 0.95 | 0.83 | 0.00 | 0.84 | 0.95 | 0.96 | 0.97 |
77
- | enteroglial cell | 771 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 0.99 |
78
- | regulatory T cell | 569 | 0.70 | 0.71 | 0.80 | 0.38 | 0.00 | 0.67 | 0.78 | 0.81 | 0.88 |
79
- | mast cell | 345 | 0.97 | 0.97 | 0.98 | 0.97 | 0.00 | 0.98 | 0.99 | 0.99 | 0.98 |
80
- | myeloid leukocyte | 323 | 0.88 | 0.90 | 0.92 | 0.90 | 0.00 | 0.94 | 0.99 | 1.00 | 0.97 |
81
- | colon endothelial cell | 311 | 0.90 | 0.88 | 0.93 | 0.93 | 0.00 | 0.90 | 0.98 | 0.98 | 0.96 |
82
- | colon macrophage | 295 | 0.82 | 0.85 | 0.86 | 0.85 | 0.00 | 0.93 | 0.99 | 1.00 | 0.94 |
83
- | transit amplifying cell of colon | 212 | 0.74 | 0.70 | 0.79 | 0.60 | 0.00 | 0.61 | 0.81 | 0.80 | 0.87 |
84
- | naive thymus-derived CD4-positive, alpha-beta T cell | 205 | 0.69 | 0.68 | 0.74 | 0.37 | 0.00 | 0.74 | 0.80 | 0.81 | 0.83 |
85
- | paneth cell of colon | 196 | 0.61 | 0.36 | 0.82 | 0.76 | 0.00 | 0.76 | 0.84 | 0.57 | 0.91 |
86
- | tuft cell of colon | 161 | 0.92 | 0.96 | 0.95 | 0.96 | 0.00 | 0.88 | 0.98 | 0.97 | 0.98 |
87
- | myofibroblast cell | 71 | 0.82 | 0.80 | 0.87 | 0.85 | 0.00 | 0.87 | 1.00 | 0.98 | 0.95 |
88
- | monocyte | 62 | 0.74 | 0.79 | 0.77 | 0.75 | 0.00 | 0.96 | 0.99 | 0.98 | 0.91 |
89
- | mature NK T cell | 41 | 0.00 | 0.37 | 0.65 | 0.38 | 0.00 | 0.46 | 0.98 | 0.96 | 0.86 |
90
- | type L enteroendocrine cell | 39 | 0.77 | 0.83 | 0.92 | 0.62 | 0.00 | 0.59 | 0.97 | 0.99 | 0.99 |
91
- | myeloid dendritic cell | 38 | 0.41 | 0.18 | 0.47 | 0.38 | 0.00 | 0.85 | 0.99 | 1.00 | 0.62 |
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- | enterochromaffin-like cell | 21 | 0.00 | 0.68 | 0.86 | 0.76 | 0.00 | 0.54 | 1.00 | 0.95 | 0.93 |
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- | natural killer cell | 13 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.79 | 1.00 | 0.96 | 0.76 |
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- | innate lymphoid cell | 11 | 0.00 | 0.00 | 0.17 | 0.00 | 0.00 | 0.54 | 0.96 | 0.96 | 0.53 |
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- | neutrophil | 9 | 0.00 | 0.00 | 0.20 | 0.46 | 0.00 | 0.78 | 1.00 | 0.95 | 0.94 |
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97
  </details>
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33
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
34
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
35
+ | enterocyte of epithelium of large intestine | 467 | 0.82 | 0.84 | 0.83 | 0.86 | 0.00 | 0.87 | 0.81 | 0.86 | 0.85 |
36
+ | CD4-positive, alpha-beta T cell | 419 | 0.84 | 0.88 | 0.87 | 0.61 | 0.00 | 0.80 | 0.84 | 0.87 | 0.90 |
37
+ | plasma cell | 315 | 0.98 | 0.98 | 0.97 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |
38
+ | CD8-positive, alpha-beta T cell | 295 | 0.80 | 0.85 | 0.83 | 0.45 | 0.00 | 0.77 | 0.82 | 0.85 | 0.88 |
39
+ | fibroblast | 236 | 0.97 | 0.97 | 0.97 | 0.96 | 0.00 | 0.96 | 0.97 | 0.97 | 0.97 |
40
+ | B cell | 225 | 0.99 | 0.98 | 0.98 | 0.98 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |
41
+ | gamma-delta T cell | 190 | 0.88 | 0.90 | 0.92 | 0.55 | 0.00 | 0.83 | 0.88 | 0.90 | 0.92 |
42
+ | intestinal crypt stem cell of colon | 152 | 0.82 | 0.86 | 0.83 | 0.79 | 0.00 | 0.78 | 0.82 | 0.82 | 0.88 |
43
+ | large intestine goblet cell | 180 | 0.92 | 0.95 | 0.94 | 0.63 | 0.00 | 0.70 | 0.92 | 0.88 | 0.92 |
44
+ | enteroglial cell | 76 | 0.99 | 0.97 | 0.97 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |
45
+ | regulatory T cell | 59 | 0.63 | 0.66 | 0.67 | 0.38 | 0.00 | 0.51 | 0.71 | 0.74 | 0.77 |
46
+ | mast cell | 46 | 0.99 | 0.98 | 0.98 | 0.96 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
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+ | myeloid leukocyte | 33 | 0.83 | 0.93 | 0.91 | 0.85 | 0.00 | 0.93 | 0.93 | 0.96 | 0.98 |
48
+ | colon endothelial cell | 38 | 0.93 | 0.90 | 0.92 | 0.89 | 0.00 | 0.90 | 0.95 | 0.96 | 0.95 |
49
+ | colon macrophage | 36 | 0.79 | 0.86 | 0.79 | 0.83 | 0.00 | 0.89 | 0.89 | 0.95 | 0.94 |
50
+ | transit amplifying cell of colon | 26 | 0.72 | 0.60 | 0.65 | 0.49 | 0.00 | 0.51 | 0.62 | 0.71 | 0.73 |
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+ | naive thymus-derived CD4-positive, alpha-beta T cell | 22 | 0.82 | 0.84 | 0.71 | 0.24 | 0.00 | 0.79 | 0.74 | 0.80 | 0.84 |
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+ | paneth cell of colon | 20 | 0.56 | 0.36 | 0.58 | 0.70 | 0.00 | 0.62 | 0.71 | 0.51 | 0.75 |
53
+ | tuft cell of colon | 18 | 0.97 | 1.00 | 1.00 | 0.88 | 0.00 | 0.82 | 0.97 | 0.92 | 0.97 |
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+ | myofibroblast cell | 8 | 0.73 | 0.84 | 0.89 | 0.86 | 0.00 | 0.94 | 1.00 | 0.84 | 0.84 |
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+ | monocyte | 4 | 0.86 | 0.86 | 0.40 | 0.67 | 0.00 | 0.86 | 0.86 | 0.86 | 0.86 |
56
+ | mature NK T cell | 6 | 0.00 | 0.25 | 0.00 | 0.29 | 0.00 | 0.18 | 0.55 | 0.60 | 0.25 |
57
+ | type L enteroendocrine cell | 3 | 0.44 | 0.67 | 0.57 | 0.80 | 0.00 | 0.44 | 0.80 | 0.40 | 0.80 |
58
+ | myeloid dendritic cell | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 |
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+ | enterochromaffin-like cell | 3 | 0.00 | 1.00 | 0.00 | 0.50 | 0.00 | 0.67 | 0.80 | 0.86 | 0.80 |
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+ | natural killer cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.18 | 0.00 | 0.00 | 0.00 |
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+ | innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.25 | 0.00 | 0.00 | 0.00 |
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  | neutrophil | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
63
 
64
  The train accuracies are computed on the training data.
65
 
66
  | Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
67
  | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
68
+ | enterocyte of epithelium of large intestine | 4100 | 0.84 | 0.85 | 0.87 | 0.91 | 0.00 | 0.89 | 0.85 | 0.89 | 0.88 |
69
+ | CD4-positive, alpha-beta T cell | 3821 | 0.85 | 0.88 | 0.91 | 0.77 | 0.00 | 0.86 | 0.87 | 0.90 | 0.92 |
70
+ | plasma cell | 2993 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
71
+ | CD8-positive, alpha-beta T cell | 2667 | 0.79 | 0.84 | 0.88 | 0.63 | 0.00 | 0.81 | 0.85 | 0.88 | 0.89 |
72
+ | fibroblast | 2361 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
73
+ | B cell | 1844 | 0.99 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
74
+ | gamma-delta T cell | 1666 | 0.91 | 0.92 | 0.95 | 0.68 | 0.00 | 0.89 | 0.92 | 0.93 | 0.96 |
75
+ | intestinal crypt stem cell of colon | 1580 | 0.84 | 0.86 | 0.91 | 0.87 | 0.00 | 0.85 | 0.90 | 0.87 | 0.92 |
76
+ | large intestine goblet cell | 1377 | 0.92 | 0.95 | 0.94 | 0.67 | 0.00 | 0.70 | 0.94 | 0.94 | 0.95 |
77
+ | enteroglial cell | 772 | 0.99 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
78
+ | regulatory T cell | 574 | 0.73 | 0.71 | 0.81 | 0.45 | 0.00 | 0.70 | 0.80 | 0.81 | 0.87 |
79
+ | mast cell | 347 | 0.98 | 0.97 | 0.98 | 0.95 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
80
+ | myeloid leukocyte | 321 | 0.85 | 0.90 | 0.92 | 0.87 | 0.00 | 0.94 | 0.99 | 1.00 | 0.96 |
81
+ | colon endothelial cell | 310 | 0.90 | 0.88 | 0.93 | 0.91 | 0.00 | 0.93 | 0.99 | 0.96 | 0.94 |
82
+ | colon macrophage | 292 | 0.79 | 0.85 | 0.86 | 0.81 | 0.00 | 0.95 | 0.99 | 1.00 | 0.94 |
83
+ | transit amplifying cell of colon | 211 | 0.75 | 0.69 | 0.81 | 0.65 | 0.00 | 0.52 | 0.80 | 0.80 | 0.87 |
84
+ | naive thymus-derived CD4-positive, alpha-beta T cell | 206 | 0.68 | 0.64 | 0.76 | 0.42 | 0.00 | 0.75 | 0.83 | 0.82 | 0.84 |
85
+ | paneth cell of colon | 197 | 0.63 | 0.35 | 0.81 | 0.78 | 0.00 | 0.79 | 0.85 | 0.58 | 0.89 |
86
+ | tuft cell of colon | 160 | 0.93 | 0.96 | 0.95 | 0.92 | 0.00 | 0.85 | 0.98 | 0.96 | 0.97 |
87
+ | myofibroblast cell | 74 | 0.82 | 0.83 | 0.88 | 0.87 | 0.00 | 0.93 | 1.00 | 0.98 | 0.95 |
88
+ | monocyte | 62 | 0.78 | 0.80 | 0.79 | 0.74 | 0.00 | 0.97 | 0.99 | 0.98 | 0.93 |
89
+ | mature NK T cell | 41 | 0.00 | 0.49 | 0.69 | 0.48 | 0.00 | 0.69 | 0.95 | 0.96 | 0.91 |
90
+ | type L enteroendocrine cell | 41 | 0.77 | 0.88 | 0.94 | 0.71 | 0.00 | 0.79 | 0.99 | 0.92 | 1.00 |
91
+ | myeloid dendritic cell | 37 | 0.00 | 0.14 | 0.45 | 0.19 | 0.00 | 0.90 | 1.00 | 1.00 | 0.75 |
92
+ | enterochromaffin-like cell | 24 | 0.00 | 0.79 | 0.88 | 0.82 | 0.00 | 0.63 | 1.00 | 0.94 | 0.96 |
93
+ | natural killer cell | 13 | 0.00 | 0.00 | 0.13 | 0.14 | 0.00 | 0.36 | 1.00 | 0.96 | 0.92 |
94
+ | innate lymphoid cell | 11 | 0.00 | 0.00 | 0.53 | 0.15 | 0.00 | 0.61 | 0.96 | 1.00 | 0.78 |
95
+ | neutrophil | 9 | 0.00 | 0.00 | 0.36 | 0.71 | 0.00 | 0.90 | 1.00 | 0.95 | 1.00 |
96
 
97
  </details>
98