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
B cell 1668 0.99 0.99 1.00 1.00 0.00 0.96 1.00 0.99 1.00
neutrophil 1522 0.99 1.00 0.99 1.00 0.00 0.98 0.99 0.99 1.00
CD8-positive, alpha-beta T cell 1071 0.81 0.91 0.92 0.91 0.00 0.80 0.80 0.81 0.89
classical monocyte 441 0.81 0.88 0.87 0.85 0.00 0.75 0.79 0.85 0.91
plasma cell 384 0.98 0.99 0.99 0.99 0.00 0.99 1.00 0.99 0.99
natural killer cell 375 0.93 0.96 0.96 0.95 0.00 0.95 0.93 0.93 0.94
monocyte 339 0.71 0.78 0.76 0.72 0.00 0.77 0.71 0.75 0.82
macrophage 277 0.91 0.94 0.95 0.93 0.00 0.93 0.93 0.91 0.95
CD4-positive, alpha-beta T cell 291 0.43 0.61 0.58 0.58 0.00 0.50 0.46 0.51 0.62
naive thymus-derived CD4-positive, alpha-beta T cell 217 0.61 0.63 0.66 0.62 0.00 0.64 0.57 0.67 0.71
endothelial cell 118 0.97 0.97 0.95 0.97 0.00 0.96 0.98 0.97 0.98
mature NK T cell 104 0.66 0.76 0.78 0.74 0.00 0.69 0.62 0.67 0.74
naive thymus-derived CD8-positive, alpha-beta T cell 60 0.45 0.29 0.61 0.25 0.00 0.50 0.49 0.46 0.59
erythrocyte 45 0.91 0.98 0.99 0.97 0.00 0.96 0.98 0.97 0.99
intermediate monocyte 32 0.00 0.00 0.21 0.09 0.00 0.21 0.27 0.33 0.42
regulatory T cell 33 0.52 0.58 0.66 0.44 0.00 0.46 0.47 0.48 0.64
innate lymphoid cell 23 0.88 0.96 0.96 0.93 0.00 0.75 0.92 0.83 0.94
T cell 13 0.69 0.71 0.64 0.77 0.00 0.45 0.59 0.51 0.73
non-classical monocyte 13 0.00 0.00 0.42 0.13 0.00 0.51 0.58 0.50 0.47
hematopoietic precursor cell 10 0.64 0.75 0.82 0.78 0.00 0.32 0.95 0.80 0.95
platelet 5 0.00 0.75 0.67 0.89 0.00 0.48 0.83 0.77 1.00
myeloid dendritic cell 2 0.00 0.00 0.67 0.67 0.00 0.02 0.80 0.67 0.50
plasmacytoid dendritic cell 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
basophil 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
hematopoietic stem 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
B cell 14889 0.99 0.99 1.00 1.00 0.00 0.96 1.00 0.99 1.00
neutrophil 13379 0.99 1.00 1.00 1.00 0.00 0.98 0.99 0.99 1.00
CD8-positive, alpha-beta T cell 9816 0.82 0.92 0.95 0.93 0.00 0.82 0.80 0.84 0.91
classical monocyte 4021 0.81 0.86 0.89 0.88 0.00 0.78 0.81 0.86 0.91
plasma cell 3592 0.99 0.98 0.99 0.99 0.00 0.99 0.99 0.99 0.99
natural killer cell 3569 0.93 0.94 0.97 0.96 0.00 0.95 0.94 0.94 0.96
monocyte 2775 0.69 0.74 0.83 0.78 0.00 0.74 0.71 0.78 0.83
macrophage 2529 0.92 0.94 0.96 0.95 0.00 0.94 0.94 0.94 0.96
CD4-positive, alpha-beta T cell 2451 0.45 0.56 0.71 0.66 0.00 0.54 0.52 0.60 0.69
naive thymus-derived CD4-positive, alpha-beta T cell 2100 0.67 0.60 0.80 0.75 0.00 0.73 0.69 0.77 0.81
endothelial cell 1232 0.98 0.98 0.98 0.98 0.00 0.98 0.99 0.99 0.98
mature NK T cell 925 0.71 0.79 0.86 0.81 0.00 0.74 0.70 0.76 0.85
naive thymus-derived CD8-positive, alpha-beta T cell 562 0.44 0.10 0.73 0.54 0.00 0.50 0.51 0.52 0.62
erythrocyte 361 0.90 0.97 0.98 0.98 0.00 0.94 0.98 0.95 0.98
intermediate monocyte 364 0.00 0.04 0.31 0.31 0.00 0.32 0.44 0.51 0.64
regulatory T cell 309 0.48 0.50 0.62 0.51 0.00 0.55 0.59 0.66 0.73
innate lymphoid cell 147 0.76 0.85 0.90 0.86 0.00 0.69 0.86 0.82 0.87
T cell 138 0.66 0.59 0.78 0.75 0.00 0.50 0.75 0.60 0.74
non-classical monocyte 113 0.00 0.02 0.54 0.29 0.00 0.62 0.66 0.71 0.71
hematopoietic precursor cell 58 0.54 0.67 0.82 0.76 0.00 0.25 0.87 0.86 0.89
platelet 49 0.00 0.58 0.74 0.93 0.00 0.57 0.84 0.86 0.95
myeloid dendritic cell 15 0.00 0.00 0.46 0.46 0.00 0.04 0.88 0.86 0.93
plasmacytoid dendritic cell 5 0.00 0.00 0.00 0.00 0.00 0.27 1.00 0.91 1.00
basophil 2 0.00 0.00 0.00 0.00 0.00 0.04 1.00 1.00 1.00
hematopoietic stem cell 2 0.00 0.00 0.00 1.00 0.00 0.01 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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