popV/tabula_sapiens_Liver

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
hepatocyte	725	0.99	0.99	0.98	0.99	0.00	0.99	1.00	0.99	1.00
macrophage	347	0.92	0.91	0.93	0.88	0.00	0.83	0.89	0.94	0.95
endothelial cell	176	0.97	0.97	0.98	0.96	0.00	0.95	0.98	0.98	0.98
monocyte	190	0.52	0.67	0.71	0.64	0.00	0.38	0.49	0.50	0.73
CD8-positive, alpha-beta T cell	135	0.84	0.84	0.86	0.74	0.00	0.80	0.75	0.84	0.87
erythrocyte	93	0.97	0.96	0.98	0.96	0.00	0.96	0.98	0.96	0.99
mature NK T cell	70	0.56	0.48	0.67	0.50	0.00	0.61	0.53	0.62	0.65
plasma cell	70	1.00	0.99	0.99	0.98	0.00	0.99	0.99	0.97	1.00
natural killer cell	81	0.65	0.68	0.68	0.68	0.00	0.67	0.66	0.73	0.71
neutrophil	72	0.94	0.83	0.76	0.83	0.00	0.89	0.95	0.92	0.95
intrahepatic cholangiocyte	55	0.98	0.97	0.97	0.99	0.00	0.96	0.97	0.96	0.99
intermediate monocyte	56	0.46	0.32	0.39	0.41	0.00	0.46	0.42	0.49	0.56
classical monocyte	39	0.14	0.05	0.09	0.16	0.00	0.28	0.25	0.30	0.16
CD4-positive, alpha-beta T cell	24	0.53	0.55	0.57	0.38	0.00	0.51	0.41	0.54	0.59
hepatic stellate cell	27	0.75	0.36	0.75	0.52	0.00	0.81	0.93	0.87	0.92
B cell	14	0.97	0.93	0.97	0.85	0.00	0.97	0.97	0.97	0.97
fibroblast	11	0.62	0.58	0.64	0.44	0.00	0.82	0.96	0.87	0.88
non-classical monocyte	13	0.65	0.42	0.65	0.57	0.00	0.51	0.65	0.65	0.71
myeloid cell	8	0.63	0.00	0.00	0.00	0.00	0.60	0.62	0.62	0.67
myeloid dendritic cell	4	0.33	0.00	0.57	0.00	0.00	0.25	0.57	0.40	0.57
hematopoietic precursor cell	6	0.00	0.29	0.29	0.29	0.00	0.46	0.67	0.50	0.29
T cell	4	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
mast cell	2	0.80	0.80	0.50	0.67	0.00	0.57	1.00	1.00	0.80
plasmacytoid dendritic 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
hepatocyte	6689	0.99	0.98	0.99	0.98	0.00	0.98	1.00	0.99	1.00
macrophage	2885	0.92	0.91	0.94	0.90	0.00	0.88	0.93	0.95	0.95
endothelial cell	1598	0.97	0.97	0.98	0.96	0.00	0.97	0.99	0.99	0.99
monocyte	1531	0.50	0.70	0.74	0.66	0.00	0.49	0.69	0.72	0.80
CD8-positive, alpha-beta T cell	1155	0.81	0.83	0.83	0.75	0.00	0.83	0.89	0.93	0.88
erythrocyte	887	0.98	0.95	0.99	0.95	0.00	0.96	0.99	0.98	0.99
mature NK T cell	738	0.61	0.61	0.70	0.62	0.00	0.73	0.84	0.88	0.82
plasma cell	696	0.98	0.98	0.98	0.96	0.00	0.99	0.99	0.99	0.99
natural killer cell	664	0.72	0.71	0.76	0.72	0.00	0.77	0.88	0.90	0.87
neutrophil	667	0.93	0.87	0.91	0.87	0.00	0.94	0.98	0.97	0.98
intrahepatic cholangiocyte	610	0.97	0.97	0.97	0.98	0.00	0.95	0.99	0.99	0.99
intermediate monocyte	501	0.45	0.44	0.55	0.46	0.00	0.61	0.74	0.77	0.77
classical monocyte	287	0.14	0.12	0.17	0.18	0.00	0.46	0.71	0.71	0.62
CD4-positive, alpha-beta T cell	267	0.57	0.58	0.57	0.43	0.00	0.68	0.86	0.87	0.75
hepatic stellate cell	196	0.78	0.28	0.71	0.68	0.00	0.85	0.98	0.98	0.96
B cell	149	0.94	0.97	0.95	0.84	0.00	0.97	0.98	0.97	0.97
fibroblast	150	0.80	0.68	0.73	0.71	0.00	0.94	0.97	0.98	0.95
non-classical monocyte	100	0.65	0.54	0.84	0.70	0.00	0.75	0.86	0.88	0.87
myeloid cell	73	0.61	0.00	0.20	0.10	0.00	0.70	0.90	0.91	0.90
myeloid dendritic cell	52	0.36	0.04	0.38	0.07	0.00	0.50	0.77	0.79	0.81
hematopoietic precursor cell	35	0.00	0.54	0.25	0.36	0.00	0.85	0.97	0.99	0.75
T cell	28	0.00	0.00	0.00	0.00	0.00	0.69	0.98	1.00	0.81
mast cell	26	0.79	0.78	0.90	0.73	0.00	0.91	0.98	0.93	0.98
plasmacytoid dendritic cell	8	0.00	0.00	0.22	0.00	0.00	0.80	1.00	1.00	0.86

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