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
neutrophil 3190 1.00 1.00 0.99 0.99 0.00 0.96 0.99 0.99 1.00
erythrocyte 1197 1.00 0.99 0.99 0.99 0.00 0.99 0.99 0.99 1.00
classical monocyte 1081 0.77 0.69 0.81 0.68 0.00 0.61 0.64 0.77 0.83
monocyte 932 0.78 0.37 0.81 0.54 0.00 0.44 0.69 0.80 0.81
CD4-positive, alpha-beta T cell 511 0.86 0.89 0.92 0.89 0.00 0.77 0.79 0.84 0.90
CD8-positive, alpha-beta T cell 469 0.55 0.66 0.66 0.68 0.00 0.59 0.61 0.65 0.65
B cell 396 0.99 0.99 0.99 0.99 0.00 0.98 0.99 0.99 0.99
natural killer cell 266 0.65 0.53 0.58 0.54 0.00 0.64 0.58 0.63 0.64
macrophage 121 0.47 0.46 0.46 0.44 0.00 0.43 0.27 0.43 0.50
intermediate monocyte 117 0.48 0.02 0.56 0.26 0.00 0.25 0.37 0.51 0.58
plasma cell 76 0.97 0.97 0.97 0.97 0.00 0.95 0.94 0.94 0.99
naive thymus-derived CD4-positive, alpha-beta T cell 48 0.42 0.12 0.47 0.29 0.00 0.30 0.39 0.49 0.50
platelet 37 0.88 0.90 0.91 0.96 0.00 0.76 0.92 0.92 0.94
non-classical monocyte 36 0.33 0.86 0.84 0.52 0.00 0.69 0.58 0.72 0.81
mature NK T cell 21 0.61 0.75 0.74 0.67 0.00 0.52 0.48 0.64 0.72
hematopoietic precursor cell 13 0.73 0.67 0.64 0.64 0.00 0.83 0.81 0.92 0.85
hematopoietic stem cell 3 0.00 0.50 0.40 0.25 0.00 0.44 0.86 0.60 0.67
basophil 2 0.50 0.00 0.40 0.67 0.00 0.02 0.17 0.50 0.50
regulatory T cell 5 0.00 0.00 0.33 0.50 0.00 0.43 0.62 0.53 0.57
plasmacytoid dendritic cell 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
common myeloid progenitor 2 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

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
neutrophil 29008 1.00 0.99 0.99 0.99 0.00 0.95 0.98 0.99 1.00
erythrocyte 10351 1.00 0.99 1.00 1.00 0.00 0.99 0.99 0.99 1.00
classical monocyte 9510 0.76 0.64 0.87 0.81 0.00 0.75 0.65 0.78 0.86
monocyte 8670 0.80 0.26 0.88 0.81 0.00 0.76 0.72 0.81 0.87
CD4-positive, alpha-beta T cell 4389 0.85 0.89 0.93 0.92 0.00 0.83 0.82 0.89 0.93
CD8-positive, alpha-beta T cell 4103 0.53 0.65 0.77 0.78 0.00 0.61 0.66 0.68 0.72
B cell 3497 0.99 0.99 0.99 0.99 0.00 0.99 0.99 0.99 0.99
natural killer cell 2791 0.68 0.58 0.73 0.73 0.00 0.67 0.65 0.68 0.74
macrophage 1107 0.48 0.43 0.59 0.60 0.00 0.49 0.40 0.53 0.63
intermediate monocyte 919 0.48 0.01 0.71 0.55 0.00 0.48 0.47 0.55 0.70
plasma cell 740 0.98 0.97 0.97 0.98 0.00 0.95 0.93 0.96 0.99
naive thymus-derived CD4-positive, alpha-beta T cell 442 0.43 0.09 0.59 0.52 0.00 0.55 0.49 0.64 0.73
platelet 401 0.91 0.93 0.95 0.99 0.00 0.83 0.97 0.97 0.96
non-classical monocyte 317 0.46 0.74 0.84 0.66 0.00 0.67 0.69 0.78 0.87
mature NK T cell 181 0.59 0.70 0.73 0.52 0.00 0.54 0.66 0.76 0.81
hematopoietic precursor cell 118 0.67 0.68 0.78 0.85 0.00 0.86 0.81 0.94 0.93
hematopoietic stem cell 61 0.00 0.31 0.68 0.80 0.00 0.80 0.98 0.97 0.96
basophil 39 0.79 0.00 0.81 0.80 0.00 0.03 0.50 0.70 0.91
regulatory T cell 35 0.00 0.00 0.69 0.29 0.00 0.34 0.71 0.62 0.77
plasmacytoid dendritic cell 28 0.70 0.73 0.79 0.81 0.00 0.86 0.90 0.86 0.93
common myeloid progenitor 1 0.00 0.00 0.00 0.00 0.00 0.00 0.67 1.00 0.00
myeloid dendritic cell 1 0.00 0.00 0.00 0.00 0.00 0.00 0.17 1.00 0.00

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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