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README.md
CHANGED
@@ -31,49 +31,49 @@ 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 |
|
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| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
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| B cell |
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| CD4-positive, alpha-beta T cell |
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| CD8-positive, alpha-beta T cell |
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| neutrophil |
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| macrophage |
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| plasma cell |
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| monocyte |
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| classical monocyte |
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| erythrocyte |
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43 |
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| natural killer cell |
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| naive thymus-derived CD4-positive, alpha-beta T cell |
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| T cell |
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46 |
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| mast cell |
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| intermediate monocyte |
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48 |
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| mature NK T cell |
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49 |
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| mononuclear phagocyte | 554 | 0.
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| CD4-positive, alpha-beta thymocyte |
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| regulatory T cell |
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52 |
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| hematopoietic precursor cell |
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53 |
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| gamma-delta T cell |
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| basophil |
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55 |
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| tissue-resident macrophage | 136 | 0.
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56 |
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| non-classical monocyte | 113 | 0.
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57 |
-
| activated CD8-positive, alpha-beta T cell |
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58 |
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| naive thymus-derived CD8-positive, alpha-beta T cell | 112 | 0.
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59 |
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| myeloid leukocyte |
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| erythroid progenitor cell |
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| innate lymphoid cell |
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| hematopoietic stem cell | 72 | 0.
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63 |
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| granulocyte |
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64 |
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| CD8-positive, alpha-beta thymocyte |
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65 |
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| activated CD4-positive, alpha-beta T cell |
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66 |
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| myeloid dendritic cell |
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67 |
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| platelet |
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68 |
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| common myeloid progenitor |
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69 |
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| thymocyte |
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70 |
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| microglial cell | 39 | 0.
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71 |
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| colon macrophage | 41 | 0.
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-
| leukocyte |
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73 |
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| plasmacytoid dendritic cell |
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74 |
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| hematopoietic cell | 8 | 0.
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75 |
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| myeloid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.
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76 |
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| Langerhans cell |
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77 |
| T follicular helper cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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78 |
| erythroid lineage cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
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@@ -81,51 +81,51 @@ The train accuracies are computed on the training data.
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| Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
|
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| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
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| B cell |
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| CD4-positive, alpha-beta T cell |
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86 |
-
| CD8-positive, alpha-beta T cell |
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87 |
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| neutrophil |
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88 |
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| macrophage |
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89 |
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| plasma cell |
|
90 |
-
| monocyte |
|
91 |
-
| classical monocyte |
|
92 |
-
| erythrocyte |
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93 |
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| natural killer cell |
|
94 |
-
| naive thymus-derived CD4-positive, alpha-beta T cell |
|
95 |
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| T cell |
|
96 |
-
| mast cell |
|
97 |
-
| intermediate monocyte |
|
98 |
-
| mature NK T cell |
|
99 |
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| mononuclear phagocyte | 4782 | 0.
|
100 |
-
| CD4-positive, alpha-beta thymocyte |
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101 |
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| regulatory T cell |
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102 |
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| hematopoietic precursor cell |
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103 |
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| gamma-delta T cell |
|
104 |
-
| basophil |
|
105 |
-
| tissue-resident macrophage | 1219 | 0.
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106 |
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| non-classical monocyte | 1171 | 0.
|
107 |
-
| activated CD8-positive, alpha-beta T cell |
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108 |
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| naive thymus-derived CD8-positive, alpha-beta T cell | 944 | 0.
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109 |
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| myeloid leukocyte |
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| erythroid progenitor cell |
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| innate lymphoid cell |
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| hematopoietic stem cell | 786 | 0.
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113 |
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| granulocyte |
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114 |
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| CD8-positive, alpha-beta thymocyte |
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| activated CD4-positive, alpha-beta T cell |
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| myeloid dendritic cell |
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| platelet |
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118 |
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| common myeloid progenitor |
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| thymocyte |
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| microglial cell | 353 | 0.
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| colon macrophage | 286 | 0.
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| leukocyte |
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123 |
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| plasmacytoid dendritic cell |
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124 |
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| hematopoietic cell | 90 | 0.
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125 |
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| myeloid cell | 79 | 0.00 | 0.00 | 0.
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126 |
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| Langerhans cell |
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127 |
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| T follicular helper cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.
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128 |
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| erythroid lineage cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.
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</details>
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31 |
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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 | 11276 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |
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35 |
+
| CD4-positive, alpha-beta T cell | 9727 | 0.55 | 0.82 | 0.83 | 0.77 | 0.00 | 0.38 | 0.42 | 0.59 | 0.79 |
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36 |
+
| CD8-positive, alpha-beta T cell | 7675 | 0.68 | 0.81 | 0.81 | 0.75 | 0.00 | 0.70 | 0.55 | 0.64 | 0.80 |
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37 |
+
| neutrophil | 6983 | 0.95 | 0.99 | 0.98 | 0.98 | 0.00 | 0.90 | 0.95 | 0.95 | 0.98 |
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+
| macrophage | 6821 | 0.81 | 0.87 | 0.91 | 0.83 | 0.00 | 0.77 | 0.72 | 0.74 | 0.90 |
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39 |
+
| plasma cell | 2790 | 0.98 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |
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40 |
+
| monocyte | 2610 | 0.59 | 0.58 | 0.76 | 0.46 | 0.00 | 0.41 | 0.47 | 0.56 | 0.68 |
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41 |
+
| classical monocyte | 1806 | 0.64 | 0.67 | 0.75 | 0.50 | 0.00 | 0.54 | 0.55 | 0.66 | 0.73 |
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42 |
+
| erythrocyte | 1496 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.97 | 0.97 | 0.98 |
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43 |
+
| natural killer cell | 1412 | 0.72 | 0.76 | 0.75 | 0.72 | 0.00 | 0.71 | 0.67 | 0.73 | 0.75 |
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44 |
+
| naive thymus-derived CD4-positive, alpha-beta T cell | 1002 | 0.23 | 0.12 | 0.30 | 0.09 | 0.00 | 0.19 | 0.22 | 0.31 | 0.29 |
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45 |
+
| T cell | 608 | 0.41 | 0.55 | 0.55 | 0.18 | 0.00 | 0.24 | 0.33 | 0.45 | 0.54 |
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46 |
+
| mast cell | 577 | 0.86 | 0.89 | 0.94 | 0.84 | 0.00 | 0.89 | 0.90 | 0.90 | 0.93 |
|
47 |
+
| intermediate monocyte | 550 | 0.33 | 0.26 | 0.52 | 0.20 | 0.00 | 0.27 | 0.31 | 0.42 | 0.49 |
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48 |
+
| mature NK T cell | 537 | 0.56 | 0.57 | 0.60 | 0.50 | 0.00 | 0.48 | 0.36 | 0.48 | 0.61 |
|
49 |
+
| mononuclear phagocyte | 554 | 0.51 | 0.02 | 0.80 | 0.13 | 0.00 | 0.08 | 0.59 | 0.55 | 0.70 |
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50 |
+
| CD4-positive, alpha-beta thymocyte | 461 | 0.37 | 0.41 | 0.61 | 0.42 | 0.00 | 0.37 | 0.33 | 0.45 | 0.60 |
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51 |
+
| regulatory T cell | 293 | 0.30 | 0.20 | 0.38 | 0.12 | 0.00 | 0.25 | 0.26 | 0.39 | 0.46 |
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52 |
+
| hematopoietic precursor cell | 209 | 0.52 | 0.76 | 0.78 | 0.69 | 0.00 | 0.46 | 0.50 | 0.57 | 0.68 |
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53 |
+
| gamma-delta T cell | 193 | 0.45 | 0.78 | 0.75 | 0.28 | 0.00 | 0.49 | 0.61 | 0.47 | 0.80 |
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54 |
+
| basophil | 166 | 0.64 | 0.65 | 0.90 | 0.41 | 0.00 | 0.66 | 0.64 | 0.73 | 0.82 |
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55 |
+
| tissue-resident macrophage | 136 | 0.67 | 0.04 | 0.84 | 0.27 | 0.00 | 0.31 | 0.53 | 0.50 | 0.77 |
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56 |
+
| non-classical monocyte | 113 | 0.29 | 0.48 | 0.46 | 0.31 | 0.00 | 0.20 | 0.24 | 0.34 | 0.54 |
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57 |
+
| activated CD8-positive, alpha-beta T cell | 113 | 0.34 | 0.33 | 0.31 | 0.03 | 0.00 | 0.09 | 0.27 | 0.30 | 0.42 |
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58 |
+
| naive thymus-derived CD8-positive, alpha-beta T cell | 112 | 0.13 | 0.02 | 0.45 | 0.14 | 0.00 | 0.15 | 0.11 | 0.15 | 0.24 |
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59 |
+
| myeloid leukocyte | 96 | 0.26 | 0.40 | 0.61 | 0.16 | 0.00 | 0.17 | 0.23 | 0.21 | 0.60 |
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60 |
+
| erythroid progenitor cell | 106 | 0.67 | 0.70 | 0.69 | 0.58 | 0.00 | 0.63 | 0.66 | 0.70 | 0.72 |
|
61 |
+
| innate lymphoid cell | 84 | 0.21 | 0.31 | 0.31 | 0.25 | 0.00 | 0.29 | 0.26 | 0.23 | 0.37 |
|
62 |
+
| hematopoietic stem cell | 72 | 0.72 | 0.78 | 0.78 | 0.69 | 0.00 | 0.68 | 0.76 | 0.76 | 0.80 |
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63 |
+
| granulocyte | 69 | 0.22 | 0.26 | 0.61 | 0.45 | 0.00 | 0.09 | 0.27 | 0.26 | 0.48 |
|
64 |
+
| CD8-positive, alpha-beta thymocyte | 70 | 0.49 | 0.62 | 0.58 | 0.54 | 0.00 | 0.54 | 0.26 | 0.42 | 0.72 |
|
65 |
+
| activated CD4-positive, alpha-beta T cell | 60 | 0.05 | 0.09 | 0.15 | 0.03 | 0.00 | 0.12 | 0.10 | 0.12 | 0.20 |
|
66 |
+
| myeloid dendritic cell | 46 | 0.11 | 0.36 | 0.41 | 0.18 | 0.00 | 0.11 | 0.13 | 0.14 | 0.21 |
|
67 |
+
| platelet | 53 | 0.68 | 0.96 | 0.98 | 0.94 | 0.00 | 0.86 | 0.81 | 0.75 | 0.96 |
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68 |
+
| common myeloid progenitor | 39 | 0.60 | 0.70 | 0.73 | 0.32 | 0.00 | 0.41 | 0.58 | 0.77 | 0.73 |
|
69 |
+
| thymocyte | 43 | 0.00 | 0.46 | 0.44 | 0.60 | 0.00 | 0.55 | 0.22 | 0.47 | 0.79 |
|
70 |
+
| microglial cell | 39 | 0.08 | 0.00 | 0.38 | 0.08 | 0.00 | 0.10 | 0.15 | 0.17 | 0.21 |
|
71 |
+
| colon macrophage | 41 | 0.31 | 0.52 | 0.77 | 0.18 | 0.00 | 0.06 | 0.23 | 0.34 | 0.72 |
|
72 |
+
| leukocyte | 15 | 0.15 | 0.32 | 0.09 | 0.11 | 0.00 | 0.05 | 0.07 | 0.15 | 0.26 |
|
73 |
+
| plasmacytoid dendritic cell | 7 | 0.00 | 0.43 | 0.43 | 0.15 | 0.00 | 0.08 | 0.29 | 0.28 | 0.44 |
|
74 |
+
| hematopoietic cell | 8 | 0.94 | 0.88 | 0.86 | 0.80 | 0.00 | 0.07 | 0.94 | 0.52 | 0.80 |
|
75 |
+
| myeloid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.13 | 0.00 | 0.00 |
|
76 |
+
| Langerhans cell | 7 | 0.37 | 0.71 | 0.55 | 0.31 | 0.00 | 0.05 | 0.35 | 0.32 | 0.67 |
|
77 |
| T follicular helper cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
|
78 |
| erythroid lineage cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
|
79 |
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|
81 |
|
82 |
| Cell Type | N cells | celltypist | knn on bbknn | knn on harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |
|
83 |
| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
|
84 |
+
| B cell | 103201 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |
|
85 |
+
| CD4-positive, alpha-beta T cell | 87384 | 0.56 | 0.82 | 0.87 | 0.82 | 0.00 | 0.42 | 0.43 | 0.59 | 0.82 |
|
86 |
+
| CD8-positive, alpha-beta T cell | 68583 | 0.68 | 0.81 | 0.87 | 0.81 | 0.00 | 0.70 | 0.55 | 0.65 | 0.82 |
|
87 |
+
| neutrophil | 62542 | 0.95 | 0.98 | 0.98 | 0.98 | 0.00 | 0.91 | 0.95 | 0.95 | 0.98 |
|
88 |
+
| macrophage | 62204 | 0.81 | 0.87 | 0.95 | 0.88 | 0.00 | 0.80 | 0.72 | 0.75 | 0.92 |
|
89 |
+
| plasma cell | 24554 | 0.98 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
|
90 |
+
| monocyte | 23139 | 0.58 | 0.54 | 0.85 | 0.68 | 0.00 | 0.59 | 0.48 | 0.56 | 0.75 |
|
91 |
+
| classical monocyte | 16393 | 0.65 | 0.66 | 0.84 | 0.71 | 0.00 | 0.67 | 0.58 | 0.68 | 0.79 |
|
92 |
+
| erythrocyte | 13112 | 0.98 | 0.97 | 0.98 | 0.99 | 0.00 | 0.98 | 0.97 | 0.97 | 0.98 |
|
93 |
+
| natural killer cell | 12819 | 0.72 | 0.76 | 0.84 | 0.80 | 0.00 | 0.73 | 0.70 | 0.74 | 0.78 |
|
94 |
+
| naive thymus-derived CD4-positive, alpha-beta T cell | 8825 | 0.24 | 0.10 | 0.47 | 0.19 | 0.00 | 0.23 | 0.24 | 0.32 | 0.38 |
|
95 |
+
| T cell | 5680 | 0.43 | 0.54 | 0.70 | 0.35 | 0.00 | 0.33 | 0.35 | 0.47 | 0.59 |
|
96 |
+
| mast cell | 5640 | 0.87 | 0.87 | 0.97 | 0.92 | 0.00 | 0.95 | 0.91 | 0.91 | 0.95 |
|
97 |
+
| intermediate monocyte | 4927 | 0.35 | 0.22 | 0.69 | 0.49 | 0.00 | 0.38 | 0.34 | 0.44 | 0.57 |
|
98 |
+
| mature NK T cell | 4854 | 0.55 | 0.55 | 0.74 | 0.60 | 0.00 | 0.54 | 0.41 | 0.50 | 0.64 |
|
99 |
+
| mononuclear phagocyte | 4782 | 0.50 | 0.01 | 0.93 | 0.46 | 0.00 | 0.77 | 0.57 | 0.55 | 0.89 |
|
100 |
+
| CD4-positive, alpha-beta thymocyte | 4224 | 0.38 | 0.37 | 0.74 | 0.50 | 0.00 | 0.53 | 0.37 | 0.45 | 0.67 |
|
101 |
+
| regulatory T cell | 2356 | 0.28 | 0.15 | 0.57 | 0.29 | 0.00 | 0.24 | 0.26 | 0.37 | 0.48 |
|
102 |
+
| hematopoietic precursor cell | 1931 | 0.53 | 0.74 | 0.86 | 0.79 | 0.00 | 0.51 | 0.57 | 0.60 | 0.76 |
|
103 |
+
| gamma-delta T cell | 1783 | 0.45 | 0.76 | 0.84 | 0.51 | 0.00 | 0.69 | 0.64 | 0.50 | 0.81 |
|
104 |
+
| basophil | 1503 | 0.63 | 0.49 | 0.95 | 0.77 | 0.00 | 0.88 | 0.67 | 0.77 | 0.89 |
|
105 |
+
| tissue-resident macrophage | 1219 | 0.70 | 0.01 | 0.90 | 0.65 | 0.00 | 0.57 | 0.56 | 0.54 | 0.79 |
|
106 |
+
| non-classical monocyte | 1171 | 0.27 | 0.41 | 0.58 | 0.53 | 0.00 | 0.26 | 0.30 | 0.42 | 0.60 |
|
107 |
+
| activated CD8-positive, alpha-beta T cell | 1029 | 0.37 | 0.27 | 0.46 | 0.18 | 0.00 | 0.41 | 0.30 | 0.31 | 0.69 |
|
108 |
+
| naive thymus-derived CD8-positive, alpha-beta T cell | 944 | 0.14 | 0.01 | 0.61 | 0.32 | 0.00 | 0.18 | 0.13 | 0.15 | 0.31 |
|
109 |
+
| myeloid leukocyte | 898 | 0.27 | 0.24 | 0.74 | 0.37 | 0.00 | 0.59 | 0.28 | 0.26 | 0.77 |
|
110 |
+
| erythroid progenitor cell | 865 | 0.66 | 0.63 | 0.82 | 0.78 | 0.00 | 0.75 | 0.76 | 0.74 | 0.80 |
|
111 |
+
| innate lymphoid cell | 887 | 0.21 | 0.29 | 0.58 | 0.47 | 0.00 | 0.50 | 0.32 | 0.28 | 0.47 |
|
112 |
+
| hematopoietic stem cell | 786 | 0.71 | 0.78 | 0.88 | 0.81 | 0.00 | 0.79 | 0.81 | 0.86 | 0.87 |
|
113 |
+
| granulocyte | 700 | 0.25 | 0.21 | 0.73 | 0.61 | 0.00 | 0.14 | 0.30 | 0.30 | 0.59 |
|
114 |
+
| CD8-positive, alpha-beta thymocyte | 661 | 0.40 | 0.53 | 0.64 | 0.54 | 0.00 | 0.61 | 0.30 | 0.46 | 0.78 |
|
115 |
+
| activated CD4-positive, alpha-beta T cell | 512 | 0.05 | 0.03 | 0.50 | 0.20 | 0.00 | 0.20 | 0.12 | 0.14 | 0.32 |
|
116 |
+
| myeloid dendritic cell | 524 | 0.13 | 0.26 | 0.60 | 0.43 | 0.00 | 0.17 | 0.19 | 0.25 | 0.31 |
|
117 |
+
| platelet | 441 | 0.74 | 0.94 | 0.97 | 0.97 | 0.00 | 0.82 | 0.87 | 0.80 | 0.97 |
|
118 |
+
| common myeloid progenitor | 417 | 0.58 | 0.58 | 0.83 | 0.73 | 0.00 | 0.77 | 0.81 | 0.89 | 0.88 |
|
119 |
+
| thymocyte | 412 | 0.00 | 0.41 | 0.55 | 0.51 | 0.00 | 0.56 | 0.25 | 0.59 | 0.90 |
|
120 |
+
| microglial cell | 353 | 0.12 | 0.16 | 0.64 | 0.25 | 0.00 | 0.28 | 0.21 | 0.21 | 0.42 |
|
121 |
+
| colon macrophage | 286 | 0.24 | 0.27 | 0.85 | 0.38 | 0.00 | 0.41 | 0.26 | 0.34 | 0.80 |
|
122 |
+
| leukocyte | 171 | 0.11 | 0.06 | 0.48 | 0.16 | 0.00 | 0.20 | 0.16 | 0.17 | 0.35 |
|
123 |
+
| plasmacytoid dendritic cell | 91 | 0.00 | 0.54 | 0.77 | 0.63 | 0.00 | 0.15 | 0.67 | 0.52 | 0.75 |
|
124 |
+
| hematopoietic cell | 90 | 0.87 | 0.74 | 0.96 | 0.79 | 0.00 | 0.07 | 0.95 | 0.62 | 0.80 |
|
125 |
+
| myeloid cell | 79 | 0.00 | 0.00 | 0.54 | 0.09 | 0.00 | 0.42 | 0.41 | 0.30 | 0.91 |
|
126 |
+
| Langerhans cell | 69 | 0.34 | 0.38 | 0.80 | 0.53 | 0.00 | 0.10 | 0.31 | 0.32 | 0.55 |
|
127 |
+
| T follicular helper cell | 6 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.02 | 0.92 | 0.55 | 0.80 |
|
128 |
+
| erythroid lineage cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 1.00 | 0.80 | 0.67 |
|
129 |
|
130 |
</details>
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131 |
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