popV/tabula_sapiens_Immune

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	11273	0.99	0.99	0.99	0.99	0.00	0.94	0.99	0.99	0.99
CD4-positive, alpha-beta T cell	9709	0.59	0.80	0.82	0.77	0.00	0.40	0.44	0.60	0.79
CD8-positive, alpha-beta T cell	7592	0.71	0.79	0.81	0.75	0.00	0.73	0.56	0.67	0.81
neutrophil	6979	0.94	0.98	0.97	0.98	0.00	0.92	0.95	0.95	0.98
macrophage	6824	0.83	0.85	0.91	0.83	0.00	0.71	0.73	0.76	0.89
plasma cell	2779	0.97	0.98	0.97	0.98	0.00	0.98	0.99	0.98	0.99
monocyte	2605	0.50	0.41	0.76	0.47	0.00	0.33	0.44	0.56	0.58
classical monocyte	1806	0.64	0.62	0.74	0.48	0.00	0.56	0.55	0.68	0.71
erythrocyte	1512	0.97	0.97	0.97	0.98	0.00	0.97	0.97	0.97	0.98
natural killer cell	1401	0.70	0.74	0.75	0.70	0.00	0.67	0.65	0.72	0.75
naive thymus-derived CD4-positive, alpha-beta T cell	1006	0.25	0.05	0.31	0.09	0.00	0.21	0.22	0.31	0.29
T cell	604	0.42	0.33	0.54	0.17	0.00	0.25	0.34	0.45	0.52
mast cell	590	0.81	0.84	0.92	0.81	0.00	0.89	0.89	0.91	0.92
intermediate monocyte	551	0.29	0.14	0.54	0.18	0.00	0.24	0.31	0.46	0.49
mature NK T cell	545	0.53	0.56	0.62	0.35	0.00	0.42	0.41	0.49	0.62
mononuclear phagocyte	556	0.57	0.00	0.75	0.15	0.00	0.03	0.59	0.57	0.63
CD4-positive, alpha-beta thymocyte	456	0.41	0.07	0.60	0.28	0.00	0.19	0.33	0.42	0.57
regulatory T cell	296	0.27	0.05	0.36	0.12	0.00	0.23	0.28	0.38	0.49
hematopoietic precursor cell	208	0.51	0.69	0.77	0.67	0.00	0.45	0.50	0.58	0.67
gamma-delta T cell	193	0.66	0.40	0.77	0.26	0.00	0.38	0.57	0.50	0.79
basophil	175	0.53	0.12	0.80	0.31	0.00	0.73	0.72	0.79	0.81
tissue-resident macrophage	128	0.68	0.00	0.83	0.21	0.00	0.24	0.67	0.52	0.76
non-classical monocyte	114	0.28	0.34	0.47	0.02	0.00	0.17	0.22	0.36	0.53
activated CD8-positive, alpha-beta T cell	119	0.34	0.00	0.38	0.04	0.00	0.09	0.25	0.38	0.39
naive thymus-derived CD8-positive, alpha-beta T cell	112	0.13	0.00	0.35	0.12	0.00	0.20	0.13	0.16	0.27
myeloid leukocyte	86	0.29	0.00	0.67	0.13	0.00	0.05	0.20	0.23	0.58
erythroid progenitor cell	107	0.64	0.65	0.67	0.60	0.00	0.61	0.65	0.67	0.72
innate lymphoid cell	83	0.17	0.18	0.31	0.25	0.00	0.26	0.17	0.23	0.33
hematopoietic stem cell	72	0.74	0.72	0.77	0.71	0.00	0.70	0.75	0.80	0.80
granulocyte	70	0.19	0.03	0.61	0.37	0.00	0.11	0.27	0.26	0.43
CD8-positive, alpha-beta thymocyte	66	0.47	0.03	0.48	0.31	0.00	0.36	0.24	0.31	0.62
activated CD4-positive, alpha-beta T cell	60	0.07	0.00	0.24	0.03	0.00	0.08	0.12	0.14	0.28
myeloid dendritic cell	44	0.14	0.14	0.33	0.32	0.00	0.13	0.12	0.14	0.21
platelet	52	0.60	0.92	0.97	0.94	0.00	0.57	0.82	0.76	0.85
common myeloid progenitor	39	0.00	0.54	0.67	0.32	0.00	0.51	0.61	0.72	0.74
thymocyte	43	0.00	0.00	0.46	0.32	0.00	0.28	0.21	0.46	0.72
microglial cell	29	0.09	0.00	0.41	0.06	0.00	0.09	0.13	0.12	0.24
colon macrophage	41	0.30	0.00	0.76	0.00	0.00	0.04	0.25	0.43	0.61
leukocyte	15	0.12	0.00	0.05	0.11	0.00	0.02	0.05	0.16	0.20
plasmacytoid dendritic cell	7	0.00	0.25	0.55	0.15	0.00	0.07	0.40	0.21	0.44
hematopoietic cell	8	0.00	0.22	0.77	0.93	0.00	0.03	1.00	0.50	1.00
myeloid cell	2	0.00	0.00	0.00	0.00	0.00	0.00	0.17	0.12	0.00
Langerhans cell	9	0.00	0.33	0.75	0.15	0.00	0.02	0.40	0.29	0.89
T follicular helper cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
erythroid lineage 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
B cell	103201	0.99	0.99	0.99	0.99	0.00	0.94	0.99	0.99	0.99
CD4-positive, alpha-beta T cell	87379	0.60	0.79	0.87	0.82	0.00	0.48	0.44	0.60	0.82
CD8-positive, alpha-beta T cell	68634	0.71	0.79	0.87	0.82	0.00	0.74	0.57	0.67	0.82
neutrophil	62532	0.95	0.98	0.98	0.98	0.00	0.92	0.95	0.95	0.98
macrophage	62168	0.82	0.84	0.94	0.87	0.00	0.77	0.73	0.76	0.92
plasma cell	24558	0.97	0.98	0.98	0.98	0.00	0.98	0.99	0.98	0.99
monocyte	23143	0.50	0.32	0.84	0.68	0.00	0.47	0.47	0.57	0.67
classical monocyte	16393	0.65	0.59	0.84	0.70	0.00	0.65	0.57	0.68	0.77
erythrocyte	13096	0.97	0.97	0.98	0.99	0.00	0.97	0.96	0.97	0.98
natural killer cell	12826	0.72	0.74	0.85	0.81	0.00	0.70	0.68	0.74	0.77
naive thymus-derived CD4-positive, alpha-beta T cell	8821	0.26	0.05	0.46	0.23	0.00	0.26	0.24	0.32	0.38
T cell	5682	0.44	0.29	0.69	0.36	0.00	0.38	0.35	0.45	0.61
mast cell	5625	0.83	0.86	0.95	0.93	0.00	0.94	0.89	0.92	0.95
intermediate monocyte	4926	0.30	0.10	0.69	0.45	0.00	0.36	0.34	0.46	0.55
mature NK T cell	4845	0.53	0.50	0.74	0.57	0.00	0.50	0.41	0.51	0.65
mononuclear phagocyte	4780	0.57	0.00	0.91	0.42	0.00	0.90	0.58	0.56	0.90
CD4-positive, alpha-beta thymocyte	4229	0.42	0.01	0.72	0.49	0.00	0.63	0.36	0.43	0.69
regulatory T cell	2353	0.26	0.03	0.55	0.28	0.00	0.24	0.26	0.38	0.48
hematopoietic precursor cell	1932	0.51	0.63	0.85	0.78	0.00	0.48	0.56	0.62	0.75
gamma-delta T cell	1783	0.66	0.28	0.86	0.39	0.00	0.52	0.58	0.50	0.82
basophil	1494	0.47	0.02	0.88	0.76	0.00	0.84	0.69	0.81	0.89
tissue-resident macrophage	1219	0.65	0.00	0.89	0.60	0.00	0.43	0.67	0.53	0.77
non-classical monocyte	1170	0.30	0.32	0.59	0.31	0.00	0.22	0.28	0.42	0.57
activated CD8-positive, alpha-beta T cell	1023	0.37	0.00	0.48	0.17	0.00	0.38	0.28	0.40	0.66
naive thymus-derived CD8-positive, alpha-beta T cell	944	0.14	0.00	0.62	0.35	0.00	0.25	0.15	0.17	0.32
myeloid leukocyte	908	0.25	0.00	0.74	0.31	0.00	0.51	0.27	0.27	0.73
erythroid progenitor cell	864	0.60	0.57	0.82	0.80	0.00	0.69	0.76	0.74	0.79
innate lymphoid cell	888	0.19	0.12	0.57	0.45	0.00	0.51	0.22	0.27	0.46
hematopoietic stem cell	786	0.72	0.69	0.86	0.81	0.00	0.76	0.81	0.84	0.86
granulocyte	699	0.22	0.00	0.74	0.67	0.00	0.17	0.29	0.30	0.56
CD8-positive, alpha-beta thymocyte	665	0.40	0.01	0.57	0.42	0.00	0.47	0.30	0.41	0.74
activated CD4-positive, alpha-beta T cell	512	0.06	0.00	0.47	0.15	0.00	0.15	0.14	0.15	0.33
myeloid dendritic cell	524	0.15	0.08	0.57	0.37	0.00	0.25	0.18	0.22	0.32
platelet	442	0.65	0.87	0.96	0.96	0.00	0.56	0.88	0.79	0.90
common myeloid progenitor	417	0.00	0.41	0.84	0.76	0.00	0.73	0.78	0.86	0.90
thymocyte	412	0.00	0.00	0.53	0.47	0.00	0.35	0.26	0.61	0.91
microglial cell	358	0.11	0.01	0.61	0.18	0.00	0.46	0.20	0.20	0.37
colon macrophage	286	0.22	0.00	0.82	0.40	0.00	0.42	0.25	0.43	0.86
leukocyte	171	0.08	0.00	0.48	0.17	0.00	0.26	0.14	0.19	0.40
plasmacytoid dendritic cell	91	0.00	0.37	0.80	0.64	0.00	0.15	0.52	0.50	0.69
hematopoietic cell	90	0.00	0.00	0.98	0.82	0.00	0.04	0.98	0.62	0.96
myeloid cell	79	0.00	0.00	0.40	0.12	0.00	0.46	0.42	0.32	0.91
Langerhans cell	67	0.00	0.05	0.75	0.46	0.00	0.02	0.36	0.29	0.74
T follicular helper cell	6	0.00	0.00	0.00	0.00	0.00	0.03	0.92	0.60	0.91
erythroid lineage cell	2	0.00	0.00	0.00	0.00	0.00	0.05	0.67	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