popV/tabula_sapiens_Lymph_Node

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
B cell	5489	0.99	1.00	1.00	1.00	0.00	0.98	0.99	0.99	1.00
CD4-positive, alpha-beta T cell	3919	0.78	0.88	0.87	0.85	0.00	0.68	0.64	0.78	0.87
CD8-positive, alpha-beta T cell	1448	0.79	0.81	0.81	0.73	0.00	0.72	0.75	0.85	0.83
plasma cell	605	0.98	0.98	0.98	0.98	0.00	0.98	0.98	0.99	0.99
naive thymus-derived CD4-positive, alpha-beta T cell	416	0.18	0.02	0.01	0.00	0.00	0.32	0.39	0.53	0.22
macrophage	167	0.91	0.92	0.91	0.89	0.00	0.85	0.87	0.90	0.91
natural killer cell	176	0.60	0.71	0.69	0.66	0.00	0.54	0.55	0.64	0.69
T cell	124	0.62	0.77	0.71	0.70	0.00	0.56	0.46	0.63	0.67
mature NK T cell	123	0.49	0.47	0.47	0.46	0.00	0.42	0.46	0.54	0.53
regulatory T cell	97	0.23	0.04	0.16	0.10	0.00	0.23	0.21	0.25	0.37
monocyte	67	0.79	0.81	0.76	0.78	0.00	0.52	0.83	0.80	0.85
innate lymphoid cell	85	0.62	0.66	0.49	0.28	0.00	0.63	0.47	0.59	0.64
classical monocyte	53	0.61	0.72	0.71	0.63	0.00	0.67	0.69	0.85	0.76
neutrophil	25	0.98	0.98	0.98	0.98	0.00	0.96	0.89	0.92	0.98
intermediate monocyte	22	0.00	0.51	0.53	0.44	0.00	0.52	0.62	0.86	0.63
mast cell	17	1.00	1.00	1.00	1.00	0.00	1.00	0.89	1.00	1.00
endothelial cell	23	0.75	0.74	0.73	0.70	0.00	0.64	0.84	0.82	0.78
myeloid dendritic cell	13	0.00	0.67	0.55	0.38	0.00	0.29	0.62	0.69	0.77
CD4-positive, alpha-beta thymocyte	10	0.00	0.00	0.00	0.00	0.00	0.20	0.10	0.42	0.00
stromal cell	12	0.65	0.63	0.77	0.83	0.00	0.71	0.88	0.92	0.80
non-classical monocyte	6	0.00	0.00	0.00	0.00	0.00	0.05	0.33	0.75	0.44
CD8-positive, alpha-beta thymocyte	3	0.00	0.00	0.00	0.00	0.00	0.12	0.36	0.44	0.50
erythrocyte	3	0.57	0.57	0.44	0.67	0.00	0.12	0.75	1.00	0.86
plasmacytoid dendritic cell	1	0.00	1.00	0.00	0.67	0.00	0.13	0.00	1.00	1.00
hematopoietic precursor cell	3	0.00	0.00	0.00	0.00	0.00	0.25	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
B cell	49257	0.99	1.00	1.00	1.00	0.00	0.98	0.99	0.99	1.00
CD4-positive, alpha-beta T cell	35361	0.78	0.88	0.88	0.87	0.00	0.70	0.65	0.79	0.88
CD8-positive, alpha-beta T cell	13234	0.79	0.84	0.84	0.76	0.00	0.74	0.78	0.85	0.85
plasma cell	5339	0.98	0.99	0.98	0.98	0.00	0.98	0.98	0.98	0.99
naive thymus-derived CD4-positive, alpha-beta T cell	3738	0.19	0.03	0.03	0.02	0.00	0.32	0.41	0.55	0.25
macrophage	1627	0.90	0.93	0.92	0.91	0.00	0.90	0.93	0.95	0.94
natural killer cell	1403	0.62	0.75	0.75	0.70	0.00	0.67	0.68	0.74	0.80
T cell	1157	0.61	0.74	0.74	0.70	0.00	0.57	0.50	0.65	0.68
mature NK T cell	901	0.50	0.50	0.55	0.49	0.00	0.57	0.61	0.70	0.72
regulatory T cell	871	0.21	0.06	0.21	0.12	0.00	0.26	0.23	0.26	0.40
monocyte	699	0.79	0.82	0.81	0.82	0.00	0.62	0.90	0.90	0.93
innate lymphoid cell	660	0.56	0.69	0.51	0.38	0.00	0.73	0.53	0.63	0.72
classical monocyte	499	0.61	0.70	0.70	0.67	0.00	0.79	0.91	0.91	0.84
neutrophil	278	0.98	0.97	0.98	0.97	0.00	0.98	0.95	0.97	0.98
intermediate monocyte	259	0.00	0.57	0.55	0.53	0.00	0.74	0.88	0.93	0.83
mast cell	195	0.97	0.97	0.96	0.96	0.00	0.96	0.94	0.98	0.97
endothelial cell	173	0.67	0.71	0.74	0.72	0.00	0.70	0.91	0.92	0.87
myeloid dendritic cell	109	0.00	0.59	0.52	0.50	0.00	0.25	0.92	0.88	0.91
CD4-positive, alpha-beta thymocyte	112	0.00	0.00	0.00	0.04	0.00	0.43	0.52	0.77	0.37
stromal cell	99	0.64	0.66	0.80	0.83	0.00	0.81	0.95	0.97	0.91
non-classical monocyte	65	0.00	0.12	0.24	0.00	0.00	0.32	0.81	0.79	0.56
CD8-positive, alpha-beta thymocyte	56	0.00	0.04	0.00	0.00	0.00	0.30	0.55	0.72	0.51
erythrocyte	39	0.57	0.84	0.73	0.78	0.00	0.17	0.93	0.88	0.93
plasmacytoid dendritic cell	15	0.00	0.74	0.81	0.75	0.00	0.28	0.83	0.97	1.00
hematopoietic precursor cell	9	0.00	0.00	0.00	0.00	0.00	0.34	0.82	0.90	0.88

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