Popular Vote (popV) model for automated cell type annotation of single-cell RNA-seq data. We provide here pretrained models for plug-in use in your own analysis. Follow our tutorial to learn how to use the model for cell type annotation.

Model description

Tabula Sapiens is a benchmark, first-draft human cell atlas of over 1.1M cells from 28 organs of 24 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects, and allows detailed analysis and comparison of cell types that are shared between tissues.

Link to CELLxGENE: Link to the data in the CELLxGENE browser for interactive exploration of the data and download of the source data.

Training Code URL: Not provided by uploader.

Metrics

We provide here accuracies for each of the experts and the ensemble model. The validation set accuracies are computed on a 10% random subset of the data that was not used for training.

Cell Type N cells celltypist knn on bbknn knn on harmony knn on scvi onclass scanvi svm xgboost Consensus Prediction
fibroblast 1252 0.97 0.96 0.98 0.98 0.00 0.94 0.97 0.97 0.98
smooth muscle cell 849 0.92 0.92 0.95 0.93 0.00 0.91 0.92 0.92 0.94
macrophage 761 0.98 0.98 0.98 0.98 0.00 0.90 0.97 0.97 0.98
endothelial cell 269 0.75 0.67 0.80 0.67 0.00 0.51 0.86 0.86 0.87
capillary endothelial cell 194 0.72 0.65 0.70 0.59 0.00 0.62 0.75 0.74 0.81
pericyte 186 0.80 0.85 0.89 0.81 0.00 0.74 0.81 0.78 0.86
CD8-positive, alpha-beta T cell 163 0.61 0.68 0.75 0.68 0.00 0.69 0.68 0.69 0.71
neutrophil 136 0.98 1.00 0.98 1.00 0.00 0.99 1.00 0.98 1.00
vein endothelial cell 80 0.66 0.46 0.56 0.44 0.00 0.50 0.66 0.65 0.72
CD4-positive, alpha-beta T cell 91 0.69 0.74 0.79 0.66 0.00 0.75 0.75 0.75 0.77
endothelial cell of artery 68 0.88 0.88 0.89 0.83 0.00 0.70 0.84 0.83 0.88
mature NK T cell 57 0.67 0.63 0.57 0.62 0.00 0.61 0.75 0.67 0.70
monocyte 45 0.89 0.88 0.85 0.82 0.00 0.70 0.81 0.80 0.87
basophil 22 0.68 0.80 0.47 0.84 0.00 0.98 1.00 0.98 0.98
natural killer cell 24 0.45 0.43 0.45 0.43 0.00 0.48 0.51 0.50 0.54
endothelial cell of lymphatic vessel 22 0.96 0.96 0.98 0.94 0.00 0.44 0.96 0.94 0.96
mast cell 17 0.00 0.67 0.38 0.83 0.00 0.92 0.97 0.94 0.94
B cell 16 0.93 0.93 0.93 0.85 0.00 0.78 1.00 0.88 0.93
erythrocyte 4 1.00 1.00 0.89 1.00 0.00 0.57 1.00 1.00 1.00
plasma cell 6 1.00 0.92 1.00 0.80 0.00 0.77 0.92 0.73 1.00
T cell 1 0.00 0.00 0.00 0.00 0.00 0.33 0.00 0.00 0.00
intermediate monocyte 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
classical monocyte 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
myeloid dendritic cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
non-classical monocyte 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

The train accuracies are computed on the training data.

Cell Type N cells celltypist knn on bbknn knn on harmony knn on scvi onclass scanvi svm xgboost Consensus Prediction
fibroblast 11445 0.97 0.95 0.99 0.98 0.00 0.95 0.97 0.97 0.98
smooth muscle cell 7738 0.91 0.89 0.97 0.96 0.00 0.92 0.93 0.92 0.95
macrophage 6757 0.97 0.98 0.98 0.99 0.00 0.91 0.97 0.98 0.99
endothelial cell 2417 0.72 0.58 0.82 0.79 0.00 0.84 0.88 0.88 0.92
capillary endothelial cell 1841 0.70 0.61 0.77 0.75 0.00 0.83 0.83 0.83 0.88
pericyte 1585 0.77 0.79 0.92 0.89 0.00 0.76 0.82 0.81 0.88
CD8-positive, alpha-beta T cell 1369 0.69 0.75 0.82 0.80 0.00 0.79 0.85 0.87 0.84
neutrophil 1303 0.99 0.98 0.98 0.99 0.00 0.98 0.99 0.99 0.99
vein endothelial cell 796 0.59 0.32 0.64 0.66 0.00 0.77 0.78 0.80 0.83
CD4-positive, alpha-beta T cell 637 0.72 0.73 0.79 0.72 0.00 0.81 0.85 0.89 0.84
endothelial cell of artery 580 0.78 0.78 0.87 0.80 0.00 0.72 0.85 0.83 0.87
mature NK T cell 458 0.70 0.70 0.77 0.75 0.00 0.80 0.90 0.88 0.85
monocyte 382 0.85 0.83 0.88 0.89 0.00 0.72 0.80 0.80 0.89
basophil 222 0.72 0.75 0.77 0.96 0.00 0.95 0.99 0.98 0.98
natural killer cell 218 0.53 0.53 0.61 0.63 0.00 0.67 0.90 0.90 0.86
endothelial cell of lymphatic vessel 176 0.95 0.96 0.97 0.97 0.00 0.40 0.98 0.96 0.97
mast cell 142 0.00 0.50 0.64 0.96 0.00 0.95 0.99 0.99 0.99
B cell 132 0.97 0.97 0.97 0.95 0.00 0.87 0.99 0.99 0.99
erythrocyte 79 0.97 0.96 0.81 0.96 0.00 0.83 0.98 0.89 0.98
plasma cell 62 0.94 0.95 0.99 0.94 0.00 0.97 1.00 1.00 1.00
T cell 15 0.00 0.00 0.61 0.26 0.00 0.41 1.00 1.00 0.93
intermediate monocyte 13 0.00 0.00 0.44 0.12 0.00 0.09 1.00 0.96 0.76
classical monocyte 12 0.00 0.00 0.55 0.56 0.00 0.65 1.00 1.00 0.96
myeloid dendritic cell 5 0.00 0.00 0.00 0.00 0.00 0.02 0.91 0.91 0.00
non-classical monocyte 1 0.00 0.00 0.00 0.00 0.00 0.20 1.00 1.00 1.00

References

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues, The Tabula Sapiens Consortium; bioRxiv, doi: https://doi.org/10.1101/2024.12.03.626516

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