popV/tabula_sapiens_Vasculature

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
fibroblast	1259	0.97	0.97	0.98	0.97	0.00	0.97	0.97	0.97	0.98
smooth muscle cell	853	0.93	0.93	0.95	0.93	0.00	0.89	0.93	0.92	0.95
macrophage	763	0.98	0.98	0.98	0.98	0.00	0.96	0.98	0.97	0.98
endothelial cell	278	0.74	0.64	0.78	0.66	0.00	0.70	0.87	0.87	0.87
capillary endothelial cell	192	0.72	0.62	0.67	0.60	0.00	0.53	0.70	0.78	0.77
pericyte	178	0.81	0.82	0.85	0.76	0.00	0.72	0.80	0.76	0.85
CD8-positive, alpha-beta T cell	158	0.55	0.69	0.76	0.69	0.00	0.65	0.66	0.69	0.67
neutrophil	132	1.00	1.00	1.00	1.00	0.00	1.00	0.99	0.99	1.00
vein endothelial cell	78	0.64	0.32	0.60	0.41	0.00	0.51	0.62	0.69	0.72
CD4-positive, alpha-beta T cell	90	0.70	0.75	0.77	0.64	0.00	0.74	0.74	0.77	0.75
endothelial cell of artery	63	0.81	0.86	0.86	0.83	0.00	0.74	0.79	0.80	0.87
mature NK T cell	56	0.68	0.72	0.70	0.73	0.00	0.72	0.69	0.72	0.72
monocyte	44	0.88	0.86	0.87	0.78	0.00	0.76	0.79	0.82	0.87
basophil	24	0.69	0.84	0.70	0.78	0.00	0.88	0.98	0.94	0.87
natural killer cell	20	0.44	0.42	0.30	0.38	0.00	0.51	0.40	0.56	0.49
endothelial cell of lymphatic vessel	21	0.98	0.98	0.98	0.95	0.00	0.88	0.95	0.95	0.98
mast cell	18	0.00	0.73	0.33	0.65	0.00	0.89	0.97	0.89	0.80
B cell	15	0.93	0.90	0.93	0.93	0.00	0.67	1.00	0.90	0.93
erythrocyte	7	1.00	0.93	1.00	1.00	0.00	1.00	1.00	1.00	1.00
plasma cell	7	1.00	0.83	0.92	0.86	0.00	0.75	1.00	0.83	1.00
T cell	1	0.00	0.00	0.00	0.00	0.00	0.29	0.00	0.00	0.00
intermediate monocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
classical monocyte	0	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
non-classical monocyte	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
fibroblast	11436	0.97	0.96	0.98	0.98	0.00	0.97	0.97	0.97	0.98
smooth muscle cell	7734	0.92	0.92	0.95	0.94	0.00	0.90	0.92	0.92	0.94
macrophage	6754	0.98	0.98	0.98	0.98	0.00	0.97	0.97	0.97	0.99
endothelial cell	2408	0.74	0.65	0.78	0.74	0.00	0.89	0.88	0.88	0.92
capillary endothelial cell	1843	0.74	0.66	0.72	0.70	0.00	0.81	0.83	0.85	0.87
pericyte	1593	0.79	0.84	0.88	0.83	0.00	0.75	0.82	0.81	0.87
CD8-positive, alpha-beta T cell	1374	0.65	0.77	0.79	0.74	0.00	0.78	0.84	0.86	0.82
neutrophil	1308	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
vein endothelial cell	797	0.57	0.37	0.57	0.55	0.00	0.77	0.78	0.81	0.81
CD4-positive, alpha-beta T cell	638	0.71	0.75	0.74	0.63	0.00	0.79	0.85	0.88	0.83
endothelial cell of artery	582	0.77	0.81	0.84	0.79	0.00	0.79	0.84	0.84	0.87
mature NK T cell	459	0.69	0.74	0.72	0.69	0.00	0.81	0.87	0.86	0.83
monocyte	383	0.84	0.87	0.86	0.83	0.00	0.85	0.78	0.79	0.87
basophil	220	0.71	0.82	0.75	0.85	0.00	0.94	0.97	0.98	0.92
natural killer cell	222	0.53	0.56	0.56	0.53	0.00	0.75	0.89	0.90	0.86
endothelial cell of lymphatic vessel	177	0.95	0.95	0.95	0.96	0.00	0.94	0.97	0.94	0.96
mast cell	141	0.00	0.66	0.46	0.72	0.00	0.96	1.00	0.99	0.92
B cell	133	0.97	0.97	0.97	0.95	0.00	0.90	0.97	0.99	0.99
erythrocyte	76	0.93	0.93	0.94	0.97	0.00	0.95	0.95	0.93	0.96
plasma cell	61	0.99	0.96	0.98	0.97	0.00	0.75	1.00	1.00	1.00
T cell	15	0.00	0.00	0.26	0.22	0.00	0.36	1.00	1.00	0.76
intermediate monocyte	13	0.00	0.00	0.00	0.00	0.00	0.30	0.96	0.90	0.87
classical monocyte	12	0.00	0.15	0.00	0.29	0.00	0.92	1.00	0.96	0.74
myeloid dendritic cell	5	0.00	0.00	0.00	0.00	0.00	0.16	0.77	0.62	0.00
non-classical monocyte	1	0.00	0.00	0.00	0.00	0.00	0.00	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