popV/tabula_sapiens_Endothelium

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
endothelial cell	3226	0.78	0.80	0.84	0.67	0.00	0.65	0.74	0.81	0.86
capillary endothelial cell	1509	0.78	0.76	0.81	0.52	0.00	0.57	0.74	0.79	0.82
cardiac endothelial cell	959	0.97	0.96	0.88	0.43	0.00	0.55	0.96	0.96	0.98
vein endothelial cell	462	0.48	0.21	0.58	0.18	0.00	0.39	0.49	0.54	0.60
endothelial cell of artery	357	0.65	0.59	0.71	0.42	0.00	0.54	0.62	0.69	0.72
endothelial cell of lymphatic vessel	224	0.66	0.68	0.73	0.62	0.00	0.58	0.60	0.66	0.66
retinal blood vessel endothelial cell	179	0.52	0.00	0.62	0.03	0.00	0.05	0.54	0.62	0.55
endothelial cell of vascular tree	77	0.45	0.03	0.45	0.17	0.00	0.47	0.47	0.70	0.78
colon endothelial cell	34	0.35	0.06	0.63	0.00	0.00	0.11	0.47	0.47	0.49
endothelial cell of arteriole	10	0.48	0.00	0.33	0.00	0.00	0.18	0.32	0.70	0.75
endothelial cell of venule	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
endothelial cell	30178	0.76	0.80	0.87	0.70	0.00	0.89	0.73	0.79	0.90
capillary endothelial cell	13774	0.78	0.75	0.82	0.57	0.00	0.82	0.74	0.79	0.85
cardiac endothelial cell	9111	0.97	0.95	0.88	0.46	0.00	0.98	0.95	0.96	0.98
vein endothelial cell	4220	0.47	0.19	0.66	0.25	0.00	0.73	0.51	0.56	0.70
endothelial cell of artery	3107	0.63	0.58	0.75	0.49	0.00	0.61	0.62	0.68	0.73
endothelial cell of lymphatic vessel	2195	0.66	0.66	0.79	0.64	0.00	0.75	0.65	0.70	0.76
retinal blood vessel endothelial cell	1882	0.50	0.00	0.66	0.07	0.00	0.98	0.58	0.63	0.83
endothelial cell of vascular tree	784	0.41	0.04	0.68	0.23	0.00	0.82	0.48	0.60	0.75
colon endothelial cell	272	0.26	0.01	0.44	0.00	0.00	0.97	0.45	0.52	0.69
endothelial cell of arteriole	107	0.45	0.00	0.35	0.00	0.00	0.57	0.41	0.80	0.88
endothelial cell of venule	43	0.00	0.00	0.00	0.00	0.00	0.21	0.45	0.62	0.75

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