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
bladder urothelial cell 2767 0.99 0.99 0.99 0.99 0.00 0.95 0.99 0.99 0.99
fibroblast 1351 0.95 0.96 0.97 0.96 0.00 0.94 0.96 0.95 0.96
monocyte 489 0.88 0.88 0.90 0.91 0.00 0.89 0.87 0.89 0.91
CD8-positive, alpha-beta T cell 407 0.84 0.87 0.88 0.81 0.00 0.86 0.85 0.89 0.89
macrophage 324 0.85 0.86 0.88 0.89 0.00 0.85 0.85 0.87 0.89
myofibroblast cell 308 0.85 0.92 0.94 0.92 0.00 0.85 0.90 0.88 0.91
CD4-positive, alpha-beta T cell 245 0.73 0.76 0.75 0.63 0.00 0.72 0.77 0.87 0.82
mast cell 159 0.99 0.99 0.99 0.98 0.00 0.97 0.98 0.97 0.99
plasma cell 134 0.93 0.96 0.98 0.97 0.00 0.94 0.97 0.97 0.95
pericyte 105 0.93 0.95 0.94 0.94 0.00 0.91 0.91 0.91 0.94
smooth muscle cell 103 0.96 0.95 0.98 0.97 0.00 0.96 0.94 0.94 0.96
T cell 70 0.30 0.24 0.38 0.24 0.00 0.50 0.42 0.56 0.55
B cell 50 0.96 0.97 0.96 0.97 0.00 0.91 0.90 0.90 0.96
vein endothelial cell 43 0.80 0.83 0.82 0.85 0.00 0.84 0.85 0.83 0.86
neutrophil 22 0.85 0.95 0.95 0.91 0.00 0.89 0.86 0.82 0.88
natural killer cell 15 0.67 0.45 0.64 0.43 0.00 0.53 0.49 0.68 0.69
endothelial cell of lymphatic vessel 12 0.85 0.83 0.83 0.70 0.00 0.30 0.88 0.80 0.88
capillary endothelial cell 11 0.47 0.67 0.53 0.52 0.00 0.74 0.75 0.74 0.82
erythrocyte 8 0.44 0.21 1.00 0.86 0.00 0.11 0.88 0.57 1.00
mature NK T cell 9 0.50 0.33 0.57 0.33 0.00 0.61 0.50 0.70 0.75
endothelial cell 7 0.00 0.00 0.20 0.40 0.00 0.42 0.20 0.20 0.25
regulatory T cell 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
bladder urothelial cell 24474 0.99 0.99 0.99 0.99 0.00 0.96 0.99 0.99 0.99
fibroblast 12415 0.95 0.96 0.98 0.97 0.00 0.94 0.95 0.95 0.97
monocyte 4366 0.89 0.90 0.95 0.94 0.00 0.90 0.90 0.91 0.94
CD8-positive, alpha-beta T cell 4025 0.87 0.87 0.92 0.88 0.00 0.89 0.88 0.92 0.92
macrophage 2828 0.83 0.86 0.93 0.91 0.00 0.86 0.87 0.89 0.92
myofibroblast cell 2828 0.85 0.89 0.94 0.93 0.00 0.85 0.88 0.88 0.91
CD4-positive, alpha-beta T cell 1944 0.71 0.71 0.81 0.72 0.00 0.76 0.84 0.89 0.85
mast cell 1409 0.99 0.98 0.99 0.99 0.00 0.97 0.98 0.97 0.99
plasma cell 1071 0.94 0.97 0.98 0.98 0.00 0.95 0.97 0.97 0.97
pericyte 1079 0.95 0.96 0.97 0.97 0.00 0.93 0.95 0.96 0.97
smooth muscle cell 950 0.96 0.95 0.97 0.97 0.00 0.95 0.96 0.95 0.96
T cell 711 0.45 0.15 0.58 0.41 0.00 0.57 0.63 0.68 0.71
B cell 434 0.93 0.95 0.96 0.95 0.00 0.92 0.92 0.95 0.96
vein endothelial cell 395 0.84 0.86 0.90 0.89 0.00 0.94 0.97 0.98 0.94
neutrophil 219 0.89 0.97 0.98 0.95 0.00 0.88 0.96 0.91 0.96
natural killer cell 150 0.63 0.29 0.71 0.57 0.00 0.66 0.74 0.77 0.80
endothelial cell of lymphatic vessel 115 0.89 0.89 0.92 0.85 0.00 0.35 0.98 0.98 0.93
capillary endothelial cell 96 0.34 0.50 0.73 0.68 0.00 0.92 0.99 0.99 0.89
erythrocyte 98 0.54 0.24 0.97 0.88 0.00 0.16 0.90 0.66 0.94
mature NK T cell 86 0.51 0.33 0.71 0.49 0.00 0.76 0.85 0.91 0.85
endothelial cell 30 0.00 0.00 0.41 0.40 0.00 0.68 0.95 0.97 0.75
regulatory T cell 23 0.00 0.00 0.23 0.23 0.00 0.28 0.94 0.92 0.30

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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