popV/tabula_sapiens_Lung

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
macrophage	1640	0.97	0.97	0.97	0.97	0.00	0.93	0.96	0.96	0.97
pulmonary alveolar type 2 cell	1146	0.97	0.98	0.98	0.97	0.00	0.97	0.98	0.97	0.98
capillary endothelial cell	695	0.96	0.96	0.97	0.96	0.00	0.95	0.96	0.96	0.97
basal cell	408	0.91	0.92	0.92	0.94	0.00	0.92	0.94	0.93	0.95
pulmonary alveolar type 1 cell	303	0.97	0.98	0.96	0.97	0.00	0.98	0.98	0.98	0.99
intermediate monocyte	287	0.66	0.64	0.71	0.68	0.00	0.64	0.75	0.86	0.77
CD4-positive, alpha-beta T cell	212	0.87	0.90	0.88	0.88	0.00	0.88	0.85	0.87	0.89
CD8-positive, alpha-beta T cell	196	0.84	0.87	0.85	0.83	0.00	0.84	0.80	0.84	0.86
endothelial cell of artery	161	0.79	0.81	0.83	0.81	0.00	0.77	0.74	0.79	0.84
club cell	172	0.78	0.85	0.87	0.83	0.00	0.82	0.85	0.83	0.88
classical monocyte	153	0.55	0.56	0.62	0.60	0.00	0.64	0.72	0.90	0.75
vein endothelial cell	140	0.83	0.81	0.83	0.84	0.00	0.84	0.80	0.86	0.88
basophil	153	0.99	0.99	0.99	0.99	0.00	0.99	0.97	0.98	0.99
lung ciliated cell	128	0.98	0.98	0.98	0.98	0.00	0.97	0.99	0.98	0.98
alveolar adventitial fibroblast	115	0.83	0.86	0.86	0.90	0.00	0.90	0.91	0.92	0.92
respiratory goblet cell	108	0.74	0.82	0.82	0.81	0.00	0.79	0.85	0.82	0.83
natural killer cell	102	0.85	0.89	0.88	0.89	0.00	0.90	0.88	0.89	0.89
pericyte	78	0.83	0.89	0.89	0.92	0.00	0.87	0.92	0.90	0.92
B cell	64	0.98	0.99	0.99	0.97	0.00	0.95	0.99	0.98	0.99
adventitial cell	61	0.83	0.84	0.78	0.84	0.00	0.83	0.85	0.89	0.89
non-classical monocyte	54	0.36	0.12	0.26	0.26	0.00	0.38	0.54	0.80	0.53
monocyte	50	0.34	0.24	0.38	0.39	0.00	0.42	0.42	0.73	0.52
neutrophil	37	0.93	0.96	0.93	0.97	0.00	0.95	0.96	0.91	0.97
endothelial cell of lymphatic vessel	30	0.95	0.94	0.94	0.94	0.00	0.95	0.98	0.97	0.97
bronchial smooth muscle cell	25	0.52	0.58	0.49	0.43	0.00	0.60	0.75	0.68	0.69
mature NK T cell	27	0.00	0.26	0.19	0.19	0.00	0.68	0.46	0.60	0.43
plasma cell	13	0.83	0.74	0.92	0.92	0.00	0.85	0.96	0.89	0.92
vascular associated smooth muscle cell	16	0.00	0.67	0.85	0.67	0.00	0.76	0.91	0.73	0.90
myeloid dendritic cell	5	0.00	0.00	0.80	0.57	0.00	0.46	0.50	1.00	0.75
pulmonary ionocyte	1	0.00	1.00	1.00	0.00	0.00	0.00	1.00	1.00	1.00
plasmacytoid dendritic cell	1	1.00	0.00	1.00	0.67	0.00	0.50	1.00	0.00	1.00
mesothelial cell	2	0.00	0.67	0.67	0.67	0.00	0.67	0.50	0.67	0.67
serous cell of epithelium of bronchus	2	0.00	0.00	0.00	0.00	0.00	0.19	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	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
macrophage	14846	0.96	0.98	0.97	0.98	0.00	0.94	0.96	0.96	0.98
pulmonary alveolar type 2 cell	10448	0.97	0.97	0.98	0.98	0.00	0.96	0.97	0.97	0.98
capillary endothelial cell	6548	0.96	0.96	0.97	0.97	0.00	0.95	0.96	0.96	0.98
basal cell	3607	0.92	0.94	0.95	0.95	0.00	0.94	0.95	0.95	0.97
pulmonary alveolar type 1 cell	2813	0.95	0.98	0.97	0.97	0.00	0.97	0.98	0.97	0.98
intermediate monocyte	2498	0.67	0.69	0.75	0.74	0.00	0.69	0.81	0.86	0.83
CD4-positive, alpha-beta T cell	1912	0.87	0.89	0.89	0.89	0.00	0.90	0.90	0.91	0.92
CD8-positive, alpha-beta T cell	1702	0.85	0.85	0.86	0.86	0.00	0.87	0.87	0.88	0.90
endothelial cell of artery	1593	0.78	0.81	0.83	0.83	0.00	0.79	0.80	0.83	0.85
club cell	1575	0.80	0.83	0.89	0.86	0.00	0.84	0.88	0.87	0.91
classical monocyte	1416	0.59	0.61	0.65	0.67	0.00	0.72	0.82	0.93	0.82
vein endothelial cell	1196	0.79	0.83	0.85	0.84	0.00	0.85	0.86	0.89	0.88
basophil	1169	0.97	0.98	0.99	0.98	0.00	0.97	0.98	0.98	0.98
lung ciliated cell	1081	0.97	0.97	0.98	0.98	0.00	0.96	0.98	0.98	0.98
alveolar adventitial fibroblast	998	0.87	0.87	0.87	0.92	0.00	0.93	0.97	0.96	0.95
respiratory goblet cell	932	0.77	0.87	0.88	0.87	0.00	0.85	0.87	0.89	0.91
natural killer cell	917	0.91	0.92	0.91	0.92	0.00	0.93	0.96	0.96	0.96
pericyte	661	0.79	0.89	0.92	0.92	0.00	0.94	0.98	0.98	0.97
B cell	599	0.97	0.97	0.97	0.98	0.00	0.99	0.99	0.98	0.99
adventitial cell	520	0.82	0.82	0.78	0.87	0.00	0.87	0.95	0.94	0.93
non-classical monocyte	473	0.27	0.11	0.22	0.19	0.00	0.52	0.71	0.80	0.62
monocyte	456	0.42	0.33	0.50	0.47	0.00	0.65	0.76	0.84	0.73
neutrophil	334	0.94	0.97	0.97	0.96	0.00	0.95	0.98	0.96	0.98
endothelial cell of lymphatic vessel	285	0.96	0.98	0.97	0.96	0.00	0.96	0.99	0.99	0.98
bronchial smooth muscle cell	195	0.51	0.60	0.68	0.56	0.00	0.78	0.91	0.93	0.90
mature NK T cell	136	0.00	0.30	0.30	0.32	0.00	0.68	0.83	0.85	0.85
plasma cell	135	0.87	0.85	0.91	0.95	0.00	0.96	0.96	0.97	0.98
vascular associated smooth muscle cell	115	0.00	0.56	0.72	0.56	0.00	0.84	0.95	0.96	0.93
myeloid dendritic cell	28	0.00	0.19	0.83	0.71	0.00	0.37	0.89	0.98	0.97
pulmonary ionocyte	24	0.00	0.92	0.86	0.83	0.00	0.79	0.92	0.94	1.00
plasmacytoid dendritic cell	18	0.90	0.00	0.95	0.84	0.00	0.65	1.00	1.00	1.00
mesothelial cell	16	0.00	0.78	0.75	0.84	0.00	0.55	0.86	0.91	0.86
serous cell of epithelium of bronchus	13	0.00	0.47	0.00	0.47	0.00	0.17	0.84	0.93	0.63
mast cell	3	0.00	0.00	0.00	0.00	0.00	0.10	1.00	0.86	0.80

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