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	scanvi	svm	xgboost	Consensus Prediction
macrophage	1632	0.96	0.97	0.98	0.98	0.94	0.96	0.96	0.98
pulmonary alveolar type 2 cell	1146	0.97	0.97	0.98	0.98	0.97	0.97	0.97	0.98
capillary endothelial cell	698	0.97	0.95	0.98	0.97	0.97	0.96	0.96	0.97
basal cell	411	0.92	0.93	0.94	0.93	0.94	0.93	0.93	0.95
pulmonary alveolar type 1 cell	302	0.98	0.99	0.98	0.98	0.98	0.99	0.98	0.99
intermediate monocyte	278	0.64	0.62	0.67	0.69	0.54	0.77	0.84	0.77
CD4-positive, alpha-beta T cell	206	0.87	0.89	0.85	0.85	0.89	0.88	0.90	0.91
CD8-positive, alpha-beta T cell	201	0.85	0.86	0.78	0.80	0.88	0.83	0.87	0.87
endothelial cell of artery	158	0.79	0.78	0.84	0.75	0.81	0.77	0.79	0.82
club cell	181	0.82	0.82	0.85	0.83	0.83	0.85	0.83	0.87
classical monocyte	154	0.58	0.57	0.61	0.61	0.57	0.73	0.89	0.74
vein endothelial cell	142	0.81	0.80	0.87	0.79	0.84	0.81	0.84	0.85
basophil	145	0.97	0.99	0.99	1.00	0.99	0.99	0.98	0.99
lung ciliated cell	134	0.97	0.99	0.99	0.99	0.96	0.98	0.98	0.98
alveolar adventitial fibroblast	117	0.85	0.86	0.86	0.90	0.90	0.91	0.91	0.94
respiratory goblet cell	107	0.76	0.82	0.83	0.80	0.84	0.83	0.83	0.84
natural killer cell	104	0.87	0.88	0.87	0.85	0.90	0.87	0.89	0.90
pericyte	76	0.79	0.86	0.88	0.89	0.90	0.90	0.92	0.92
B cell	67	0.98	0.98	0.98	0.99	0.98	0.98	0.98	0.99
adventitial cell	61	0.68	0.83	0.81	0.85	0.85	0.87	0.88	0.90
non-classical monocyte	55	0.32	0.11	0.34	0.06	0.36	0.56	0.77	0.55
monocyte	51	0.42	0.33	0.38	0.46	0.32	0.48	0.72	0.58
neutrophil	35	0.92	0.97	0.94	0.94	0.96	0.97	0.89	0.96
endothelial cell of lymphatic vessel	32	0.96	0.97	0.92	0.96	0.94	0.97	0.97	0.98
bronchial smooth muscle cell	24	0.49	0.48	0.69	0.51	0.54	0.64	0.78	0.73
mature NK T cell	27	0.00	0.25	0.31	0.21	0.56	0.48	0.51	0.45
plasma cell	12	0.87	0.85	0.92	0.96	0.92	0.89	0.92	0.96
vascular associated smooth muscle cell	18	0.53	0.52	0.47	0.64	0.79	0.76	0.75	0.73
myeloid dendritic cell	6	0.00	0.00	0.83	0.80	0.77	0.67	0.92	0.91
pulmonary ionocyte	1	0.00	0.00	0.00	0.00	0.50	1.00	1.00	0.00
plasmacytoid dendritic cell	1	0.00	0.00	1.00	0.67	0.40	1.00	1.00	1.00
mesothelial cell	1	0.00	0.50	0.50	0.50	0.40	0.40	0.50	0.50
serous cell of epithelium of bronchus	2	0.00	0.00	0.00	0.00	0.40	0.80	1.00	0.00
mast cell	0	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	scanvi	svm	xgboost	Consensus Prediction
macrophage	14854	0.96	0.98	0.98	0.98	0.94	0.96	0.96	0.98
pulmonary alveolar type 2 cell	10448	0.97	0.97	0.99	0.98	0.97	0.97	0.97	0.98
capillary endothelial cell	6545	0.97	0.96	0.98	0.98	0.97	0.96	0.96	0.98
basal cell	3604	0.92	0.94	0.96	0.96	0.94	0.95	0.95	0.97
pulmonary alveolar type 1 cell	2814	0.98	0.97	0.98	0.98	0.97	0.98	0.97	0.98
intermediate monocyte	2507	0.62	0.62	0.78	0.78	0.63	0.81	0.87	0.83
CD4-positive, alpha-beta T cell	1918	0.87	0.87	0.90	0.90	0.91	0.90	0.92	0.93
CD8-positive, alpha-beta T cell	1697	0.85	0.83	0.87	0.87	0.89	0.87	0.90	0.91
endothelial cell of artery	1596	0.78	0.79	0.86	0.85	0.82	0.82	0.83	0.86
club cell	1566	0.82	0.82	0.91	0.90	0.86	0.88	0.86	0.91
classical monocyte	1415	0.60	0.56	0.72	0.71	0.71	0.81	0.93	0.84
vein endothelial cell	1194	0.81	0.81	0.88	0.86	0.85	0.86	0.89	0.88
basophil	1177	0.97	0.98	0.99	0.99	0.98	0.98	0.98	0.98
lung ciliated cell	1075	0.96	0.97	0.99	0.99	0.95	0.98	0.98	0.98
alveolar adventitial fibroblast	996	0.87	0.85	0.89	0.94	0.93	0.96	0.97	0.96
respiratory goblet cell	933	0.80	0.86	0.89	0.89	0.87	0.88	0.88	0.91
natural killer cell	915	0.90	0.91	0.93	0.93	0.94	0.95	0.96	0.96
pericyte	663	0.78	0.89	0.94	0.92	0.95	0.98	0.98	0.97
B cell	596	0.98	0.97	0.98	0.98	0.98	0.99	0.98	0.99
adventitial cell	520	0.75	0.80	0.83	0.91	0.91	0.95	0.96	0.95
non-classical monocyte	472	0.26	0.08	0.34	0.30	0.45	0.71	0.80	0.68
monocyte	455	0.43	0.27	0.53	0.53	0.49	0.76	0.83	0.77
neutrophil	336	0.93	0.97	0.98	0.96	0.97	0.99	0.95	0.99
endothelial cell of lymphatic vessel	283	0.96	0.98	0.98	0.98	0.97	0.99	0.99	0.98
bronchial smooth muscle cell	196	0.50	0.55	0.77	0.60	0.80	0.91	0.95	0.91
mature NK T cell	136	0.00	0.15	0.53	0.40	0.70	0.83	0.91	0.91
plasma cell	136	0.81	0.83	0.95	0.94	0.94	0.97	0.94	0.98
vascular associated smooth muscle cell	113	0.48	0.50	0.75	0.61	0.83	0.95	0.95	0.94
myeloid dendritic cell	27	0.00	0.12	0.84	0.73	0.77	0.93	0.90	0.96
pulmonary ionocyte	24	0.00	0.89	0.98	0.88	0.79	0.96	0.94	0.96
plasmacytoid dendritic cell	18	0.00	0.00	0.95	0.95	0.86	0.97	0.97	0.97
mesothelial cell	17	0.00	0.79	0.81	0.77	0.60	0.92	0.87	0.83
serous cell of epithelium of bronchus	13	0.00	0.00	0.64	0.27	0.68	0.90	0.93	0.70
mast cell	3	0.00	0.00	0.00	0.00	0.29	1.00	0.86	0.50

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

popV
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tabula_sapiens_Lung

Model description

Metrics

References

Collection including popV/tabula_sapiens_Lung

Tabula Sapiens