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
B cell 5485 1.00 1.00 1.00 1.00 0.00 0.99 0.99 0.99 1.00
CD4-positive, alpha-beta T cell 3937 0.76 0.88 0.86 0.85 0.00 0.56 0.63 0.78 0.86
CD8-positive, alpha-beta T cell 1453 0.79 0.81 0.80 0.75 0.00 0.73 0.76 0.84 0.84
plasma cell 604 0.98 0.98 0.98 0.99 0.00 0.99 0.99 0.98 0.99
naive thymus-derived CD4-positive, alpha-beta T cell 415 0.21 0.04 0.05 0.06 0.00 0.28 0.38 0.55 0.32
macrophage 162 0.91 0.91 0.89 0.88 0.00 0.85 0.86 0.89 0.92
natural killer cell 176 0.62 0.73 0.68 0.63 0.00 0.67 0.54 0.64 0.71
T cell 121 0.62 0.76 0.68 0.64 0.00 0.57 0.47 0.63 0.67
mature NK T cell 116 0.48 0.46 0.50 0.47 0.00 0.48 0.48 0.55 0.58
regulatory T cell 93 0.23 0.00 0.09 0.07 0.00 0.15 0.19 0.23 0.34
monocyte 69 0.78 0.83 0.76 0.74 0.00 0.74 0.78 0.83 0.88
innate lymphoid cell 85 0.61 0.65 0.48 0.40 0.00 0.49 0.55 0.64 0.65
classical monocyte 52 0.69 0.74 0.66 0.59 0.00 0.74 0.68 0.81 0.78
neutrophil 27 0.87 0.96 0.98 1.00 0.00 0.95 0.94 0.89 0.95
intermediate monocyte 22 0.47 0.51 0.38 0.30 0.00 0.47 0.67 0.83 0.70
mast cell 17 1.00 1.00 0.97 0.97 0.00 0.92 1.00 1.00 1.00
endothelial cell 24 0.74 0.80 0.72 0.67 0.00 0.73 0.84 0.71 0.81
myeloid dendritic cell 13 0.59 0.64 0.55 0.11 0.00 0.34 0.55 0.73 0.69
CD4-positive, alpha-beta thymocyte 9 0.00 0.00 0.00 0.00 0.00 0.21 0.16 0.24 0.00
stromal cell 12 0.80 0.70 0.74 0.64 0.00 0.75 0.88 0.88 0.89
non-classical monocyte 6 0.00 0.00 0.29 0.00 0.00 0.07 0.31 0.92 0.25
CD8-positive, alpha-beta thymocyte 3 0.00 0.00 0.00 0.00 0.00 0.06 0.44 0.36 0.00
erythrocyte 2 0.40 0.50 0.29 0.67 0.00 0.36 0.80 1.00 1.00
plasmacytoid dendritic cell 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.67 0.00
hematopoietic precursor cell 3 0.00 0.00 0.50 0.40 0.00 0.22 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
B cell 49261 1.00 1.00 1.00 1.00 0.00 0.99 1.00 0.99 1.00
CD4-positive, alpha-beta T cell 35343 0.74 0.88 0.89 0.88 0.00 0.59 0.63 0.79 0.87
CD8-positive, alpha-beta T cell 13229 0.78 0.82 0.86 0.81 0.00 0.75 0.78 0.86 0.85
plasma cell 5340 0.98 0.98 0.99 0.99 0.00 0.98 0.99 0.99 0.99
naive thymus-derived CD4-positive, alpha-beta T cell 3739 0.21 0.01 0.18 0.16 0.00 0.29 0.39 0.56 0.35
macrophage 1632 0.91 0.92 0.93 0.92 0.00 0.89 0.93 0.95 0.94
natural killer cell 1403 0.63 0.72 0.79 0.75 0.00 0.73 0.71 0.75 0.81
T cell 1160 0.62 0.72 0.77 0.73 0.00 0.59 0.48 0.67 0.69
mature NK T cell 908 0.50 0.44 0.64 0.63 0.00 0.59 0.60 0.68 0.73
regulatory T cell 875 0.22 0.01 0.39 0.25 0.00 0.19 0.23 0.26 0.39
monocyte 697 0.78 0.79 0.84 0.84 0.00 0.83 0.87 0.92 0.93
innate lymphoid cell 660 0.57 0.64 0.58 0.55 0.00 0.70 0.59 0.67 0.73
classical monocyte 500 0.58 0.67 0.72 0.69 0.00 0.82 0.86 0.91 0.86
neutrophil 276 0.86 0.96 0.99 0.96 0.00 0.96 1.00 0.97 0.97
intermediate monocyte 259 0.50 0.51 0.63 0.57 0.00 0.77 0.89 0.93 0.85
mast cell 195 0.97 0.97 0.96 0.96 0.00 0.92 0.98 0.98 0.97
endothelial cell 172 0.67 0.65 0.74 0.72 0.00 0.73 0.96 0.93 0.88
myeloid dendritic cell 109 0.50 0.52 0.62 0.50 0.00 0.29 0.90 0.95 0.87
CD4-positive, alpha-beta thymocyte 113 0.00 0.00 0.08 0.20 0.00 0.42 0.47 0.78 0.55
stromal cell 99 0.84 0.51 0.85 0.77 0.00 0.71 0.98 0.97 0.95
non-classical monocyte 65 0.00 0.06 0.26 0.14 0.00 0.39 0.74 0.84 0.57
CD8-positive, alpha-beta thymocyte 56 0.00 0.00 0.04 0.07 0.00 0.29 0.74 0.65 0.63
erythrocyte 40 0.82 0.82 0.67 0.84 0.00 0.51 0.92 0.93 0.95
plasmacytoid dendritic cell 15 0.00 0.70 0.81 0.81 0.00 0.23 0.97 0.97 0.97
hematopoietic precursor cell 9 0.00 0.00 0.59 0.38 0.00 0.44 0.95 0.95 0.89

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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