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
conjunctival epithelial cell 1126 0.96 0.94 0.96 0.97 0.00 0.88 0.96 0.96 0.97
corneal epithelial cell 389 0.95 0.84 0.95 0.95 0.00 0.95 0.95 0.93 0.96
B cell 438 0.99 0.99 0.99 0.99 0.00 1.00 1.00 0.99 1.00
retinal blood vessel endothelial cell 199 0.97 0.96 0.97 0.97 0.00 0.94 0.98 0.98 0.98
CD4-positive, alpha-beta T cell 175 0.91 0.92 0.91 0.81 0.00 0.84 0.90 0.91 0.93
fibroblast 164 0.82 0.75 0.76 0.72 0.00 0.65 0.80 0.81 0.84
eye photoreceptor cell 142 0.94 0.96 0.96 0.95 0.00 0.95 0.95 0.96 0.96
plasma cell 132 0.95 0.92 0.95 0.97 0.00 0.93 0.98 0.95 0.96
acinar cell 135 0.91 0.93 0.97 0.96 0.00 0.93 0.90 0.94 0.94
keratocyte 81 0.63 0.61 0.63 0.58 0.00 0.64 0.74 0.75 0.75
CD8-positive, alpha-beta T cell 83 0.78 0.81 0.80 0.58 0.00 0.75 0.82 0.82 0.82
myeloid leukocyte 80 0.79 0.82 0.80 0.75 0.00 0.69 0.81 0.80 0.84
Mueller cell 54 0.81 0.85 0.83 0.83 0.00 0.89 0.85 0.86 0.87
smooth muscle cell 47 0.94 0.97 0.98 0.92 0.00 0.90 0.96 0.93 0.96
microglial cell 33 0.73 0.74 0.71 0.60 0.00 0.64 0.70 0.67 0.76
Schwann cell 32 0.90 0.84 0.87 0.84 0.00 0.79 0.85 0.84 0.84
macrophage 23 0.00 0.40 0.47 0.43 0.00 0.53 0.68 0.65 0.58
erythrocyte 15 0.97 0.97 0.97 1.00 0.00 0.94 1.00 0.91 0.97
muscle cell 12 0.92 0.91 0.96 0.75 0.00 0.83 0.96 1.00 1.00
monocyte 10 0.61 0.73 0.64 0.27 0.00 0.63 0.13 0.60 0.67
mature NK T cell 5 0.00 0.33 0.57 0.33 0.00 0.47 0.80 0.67 0.75
retinal pigment epithelial cell 9 0.94 0.94 0.94 0.88 0.00 0.82 1.00 0.88 0.94
T cell 3 0.00 0.00 0.00 0.00 0.00 0.00 0.15 0.00 0.00
retinal bipolar neuron 3 0.50 0.40 0.40 0.33 0.00 0.57 0.40 0.40 0.33
natural killer cell 5 0.00 0.57 0.50 0.29 0.00 0.57 0.57 0.29 0.57
neutrophil 5 0.91 0.77 0.89 0.89 0.00 0.83 0.89 0.67 1.00
adipocyte 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
mast cell 3 0.60 0.67 0.80 0.57 0.00 0.67 0.86 1.00 0.86
intermediate monocyte 2 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.40 0.00
myeloid dendritic cell 1 0.00 0.00 0.00 0.00 0.00 0.33 0.00 0.00 0.00
classical monocyte 4 0.00 0.00 0.00 0.00 0.00 0.17 0.00 0.00 0.00
radial glial cell 2 0.00 0.00 0.00 0.00 0.00 0.04 0.00 0.00 0.00
endothelial cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
basophil 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
retina horizontal cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
stromal cell 0 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
erythroid lineage 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
retinal ganglion 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
conjunctival epithelial cell 9959 0.96 0.92 0.98 0.97 0.00 0.90 0.97 0.96 0.98
corneal epithelial cell 3798 0.94 0.77 0.96 0.96 0.00 0.94 0.96 0.94 0.96
B cell 3715 0.98 0.98 0.99 0.99 0.00 0.99 1.00 0.99 1.00
retinal blood vessel endothelial cell 1892 0.97 0.96 0.98 0.98 0.00 0.96 0.99 0.98 0.99
CD4-positive, alpha-beta T cell 1438 0.86 0.86 0.90 0.85 0.00 0.88 0.93 0.94 0.93
fibroblast 1424 0.80 0.70 0.88 0.81 0.00 0.78 0.88 0.89 0.90
eye photoreceptor cell 1392 0.94 0.94 0.97 0.97 0.00 0.96 0.98 0.98 0.98
plasma cell 1215 0.95 0.91 0.98 0.95 0.00 0.95 0.99 0.98 0.99
acinar cell 1210 0.90 0.90 0.98 0.97 0.00 0.92 0.93 0.94 0.95
keratocyte 905 0.73 0.63 0.85 0.76 0.00 0.81 0.87 0.88 0.89
CD8-positive, alpha-beta T cell 853 0.79 0.79 0.84 0.75 0.00 0.85 0.90 0.91 0.90
myeloid leukocyte 568 0.76 0.74 0.83 0.84 0.00 0.88 0.97 0.97 0.94
Mueller cell 451 0.80 0.78 0.88 0.86 0.00 0.90 0.94 0.95 0.92
smooth muscle cell 408 0.93 0.93 0.97 0.95 0.00 0.91 0.97 0.97 0.97
microglial cell 375 0.73 0.74 0.81 0.75 0.00 0.86 0.99 0.98 0.93
Schwann cell 251 0.87 0.85 0.89 0.91 0.00 0.82 0.94 0.94 0.92
macrophage 131 0.00 0.20 0.62 0.64 0.00 0.79 0.98 0.99 0.94
erythrocyte 133 0.94 0.92 0.99 0.99 0.00 0.99 1.00 0.99 0.99
muscle cell 130 0.78 0.63 0.94 0.89 0.00 0.89 0.96 0.96 0.97
monocyte 76 0.40 0.49 0.62 0.58 0.00 0.89 0.97 1.00 0.90
mature NK T cell 67 0.00 0.06 0.39 0.08 0.00 0.82 0.94 0.96 0.64
retinal pigment epithelial cell 58 0.98 0.98 0.98 0.97 0.00 0.94 1.00 1.00 0.98
T cell 60 0.00 0.00 0.11 0.00 0.00 0.54 0.83 0.88 0.67
retinal bipolar neuron 58 0.86 0.84 0.90 0.80 0.00 0.83 0.99 0.95 0.92
natural killer cell 49 0.00 0.40 0.61 0.52 0.00 0.79 0.91 0.91 0.91
neutrophil 46 0.87 0.72 0.85 0.91 0.00 0.68 1.00 0.97 0.98
adipocyte 38 0.00 0.00 0.79 0.53 0.00 0.48 0.83 0.85 0.86
mast cell 33 0.70 0.73 0.79 0.72 0.00 0.80 1.00 0.96 0.94
intermediate monocyte 28 0.00 0.00 0.50 0.36 0.00 0.45 1.00 1.00 0.86
myeloid dendritic cell 27 0.00 0.29 0.62 0.33 0.00 0.56 0.90 0.93 0.86
classical monocyte 15 0.00 0.00 0.22 0.32 0.00 0.39 1.00 1.00 0.89
radial glial cell 11 0.00 0.00 0.00 0.00 0.00 0.03 0.58 0.63 0.95
endothelial cell 13 0.00 0.00 0.21 0.00 0.00 0.16 0.90 0.84 0.63
basophil 5 0.00 0.00 0.44 0.29 0.00 0.62 1.00 1.00 0.75
retina horizontal cell 5 0.00 0.00 0.00 0.00 0.00 0.20 1.00 1.00 1.00
stromal cell 3 0.00 0.00 0.00 0.00 0.00 0.10 1.00 0.67 0.80
erythroid lineage cell 2 0.00 0.00 0.00 0.00 0.00 1.00 1.00 1.00 0.67
non-classical monocyte 2 0.00 0.00 0.00 0.00 0.00 0.40 1.00 1.00 0.67
retinal ganglion cell 1 0.00 0.00 0.00 0.00 0.00 0.25 1.00 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

Downloads last month

-

Downloads are not tracked for this model. How to track
Inference API
Unable to determine this model’s pipeline type. Check the docs .

Collection including popV/tabula_sapiens_Eye