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 bbknn knn harmony knn on scvi onclass scanvi svm xgboost Consensus Prediction
acinar cell of salivary gland 1210 0.96 0.94 0.97 0.96 0.00 0.91 0.97 0.97 0.98
B cell 532 1.00 0.99 0.99 0.99 0.00 0.99 1.00 0.99 1.00
fibroblast 455 0.97 0.94 0.97 0.94 0.00 0.96 0.96 0.96 0.97
CD8-positive, alpha-beta T cell 385 0.92 0.89 0.94 0.91 0.00 0.90 0.90 0.91 0.94
duct epithelial cell 385 0.87 0.78 0.94 0.84 0.00 0.77 0.88 0.89 0.91
CD4-positive, alpha-beta T cell 175 0.89 0.87 0.87 0.87 0.00 0.86 0.88 0.90 0.91
endothelial cell 160 0.95 0.90 0.95 0.90 0.00 0.94 0.94 0.93 0.96
macrophage 169 0.91 0.72 0.92 0.82 0.00 0.90 0.94 0.95 0.95
basal cell 101 0.89 0.91 0.93 0.88 0.00 0.86 0.87 0.90 0.91
tissue-resident macrophage 76 0.88 0.00 0.89 0.67 0.00 0.82 0.89 0.90 0.95
plasma cell 49 0.92 0.96 0.94 0.98 0.00 0.96 0.98 0.96 0.98
endothelial cell of lymphatic vessel 48 0.89 0.72 0.92 0.74 0.00 0.84 0.87 0.84 0.93
adventitial cell 56 0.86 0.24 0.76 0.62 0.00 0.75 0.79 0.80 0.83
vascular associated smooth muscle cell 48 0.99 0.99 0.97 0.95 0.00 0.97 0.98 0.98 0.99
neutrophil 23 0.94 0.90 1.00 0.94 0.00 0.94 0.98 0.98 0.96
myoepithelial cell 22 0.91 0.84 0.91 0.91 0.00 0.81 0.88 0.86 0.92
T cell 24 0.60 0.15 0.51 0.56 0.00 0.47 0.53 0.59 0.62
ionocyte 14 0.75 0.75 0.88 0.60 0.00 0.63 0.86 0.81 0.85
endothelial cell of artery 9 0.67 0.56 0.62 0.46 0.00 0.59 0.90 0.67 0.78
monocyte 12 0.55 0.57 0.52 0.48 0.00 0.57 0.65 0.58 0.59
natural killer cell 7 0.50 0.62 0.77 0.40 0.00 0.50 0.61 0.52 0.71
mast cell 4 0.00 0.73 0.60 0.67 0.00 0.67 0.57 0.80 0.67
classical monocyte 8 0.00 0.00 0.17 0.31 0.00 0.12 0.22 0.17 0.00
intermediate monocyte 8 0.00 0.00 0.17 0.31 0.00 0.00 0.17 0.18 0.00
mature NK T cell 2 0.00 0.00 0.00 0.00 0.00 0.57 0.00 0.00 0.00
leukocyte 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
pericyte 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
salivary gland cell 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 bbknn knn harmony knn on scvi onclass scanvi svm xgboost Consensus Prediction
acinar cell of salivary gland 11027 0.96 0.93 0.98 0.97 0.00 0.94 0.96 0.96 0.98
B cell 4416 0.99 0.99 0.99 0.99 0.00 0.99 1.00 0.99 1.00
fibroblast 4012 0.97 0.94 0.98 0.97 0.00 0.97 0.97 0.97 0.99
CD8-positive, alpha-beta T cell 3680 0.91 0.86 0.95 0.93 0.00 0.90 0.91 0.92 0.94
duct epithelial cell 3504 0.86 0.75 0.95 0.90 0.00 0.82 0.87 0.88 0.92
CD4-positive, alpha-beta T cell 1711 0.89 0.85 0.92 0.89 0.00 0.89 0.90 0.91 0.92
endothelial cell 1469 0.94 0.88 0.96 0.94 0.00 0.96 0.97 0.97 0.98
macrophage 1454 0.89 0.71 0.95 0.95 0.00 0.96 0.97 0.98 0.98
basal cell 1081 0.92 0.92 0.96 0.93 0.00 0.91 0.95 0.94 0.96
tissue-resident macrophage 578 0.81 0.00 0.93 0.92 0.00 0.88 0.89 0.90 0.94
plasma cell 534 0.94 0.96 0.98 0.98 0.00 0.97 0.99 0.98 0.99
endothelial cell of lymphatic vessel 498 0.91 0.66 0.94 0.88 0.00 0.93 0.94 0.95 0.97
adventitial cell 404 0.84 0.21 0.87 0.74 0.00 0.80 0.81 0.82 0.94
vascular associated smooth muscle cell 355 0.96 0.96 0.96 0.98 0.00 0.97 0.96 0.97 0.97
neutrophil 220 0.93 0.91 0.97 0.93 0.00 0.93 0.98 0.96 0.97
myoepithelial cell 194 0.91 0.90 0.94 0.93 0.00 0.80 0.90 0.90 0.94
T cell 169 0.65 0.23 0.76 0.71 0.00 0.64 0.82 0.85 0.87
ionocyte 128 0.88 0.86 0.93 0.70 0.00 0.73 0.93 0.88 0.94
endothelial cell of artery 107 0.76 0.60 0.92 0.58 0.00 0.82 0.93 0.92 0.92
monocyte 87 0.50 0.51 0.66 0.58 0.00 0.81 0.88 0.93 0.88
natural killer cell 66 0.44 0.42 0.61 0.48 0.00 0.47 0.55 0.63 0.69
mast cell 41 0.00 0.73 0.73 0.64 0.00 0.86 1.00 0.99 0.99
classical monocyte 35 0.00 0.00 0.44 0.37 0.00 0.80 0.99 0.99 0.87
intermediate monocyte 34 0.00 0.00 0.55 0.48 0.00 0.77 0.92 0.94 0.94
mature NK T cell 21 0.00 0.00 0.09 0.31 0.00 0.54 0.84 0.79 0.69
leukocyte 6 0.00 0.00 0.92 0.57 0.00 0.55 1.00 1.00 1.00
pericyte 3 0.00 0.00 0.33 0.57 0.00 0.00 1.00 1.00 0.50
salivary gland cell 2 0.00 0.00 0.00 0.00 0.00 0.07 1.00 0.80 0.67
myeloid dendritic cell 1 0.00 0.00 0.00 0.00 0.00 0.50 0.50 1.00 0.00
non-classical monocyte 1 0.00 0.00 0.00 0.00 0.00 0.50 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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