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 on bbknn	knn on harmony	knn on scvi	onclass	scanvi	svm	xgboost	Consensus Prediction
B cell	11276	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
CD4-positive, alpha-beta T cell	9727	0.55	0.82	0.83	0.77	0.00	0.38	0.42	0.59	0.79
CD8-positive, alpha-beta T cell	7675	0.68	0.81	0.81	0.75	0.00	0.70	0.55	0.64	0.80
neutrophil	6983	0.95	0.99	0.98	0.98	0.00	0.90	0.95	0.95	0.98
macrophage	6821	0.81	0.87	0.91	0.83	0.00	0.77	0.72	0.74	0.90
plasma cell	2790	0.98	0.99	0.98	0.98	0.00	0.98	0.98	0.98	0.99
monocyte	2610	0.59	0.58	0.76	0.46	0.00	0.41	0.47	0.56	0.68
classical monocyte	1806	0.64	0.67	0.75	0.50	0.00	0.54	0.55	0.66	0.73
erythrocyte	1496	0.98	0.98	0.98	0.98	0.00	0.98	0.97	0.97	0.98
natural killer cell	1412	0.72	0.76	0.75	0.72	0.00	0.71	0.67	0.73	0.75
naive thymus-derived CD4-positive, alpha-beta T cell	1002	0.23	0.12	0.30	0.09	0.00	0.19	0.22	0.31	0.29
T cell	608	0.41	0.55	0.55	0.18	0.00	0.24	0.33	0.45	0.54
mast cell	577	0.86	0.89	0.94	0.84	0.00	0.89	0.90	0.90	0.93
intermediate monocyte	550	0.33	0.26	0.52	0.20	0.00	0.27	0.31	0.42	0.49
mature NK T cell	537	0.56	0.57	0.60	0.50	0.00	0.48	0.36	0.48	0.61
mononuclear phagocyte	554	0.51	0.02	0.80	0.13	0.00	0.08	0.59	0.55	0.70
CD4-positive, alpha-beta thymocyte	461	0.37	0.41	0.61	0.42	0.00	0.37	0.33	0.45	0.60
regulatory T cell	293	0.30	0.20	0.38	0.12	0.00	0.25	0.26	0.39	0.46
hematopoietic precursor cell	209	0.52	0.76	0.78	0.69	0.00	0.46	0.50	0.57	0.68
gamma-delta T cell	193	0.45	0.78	0.75	0.28	0.00	0.49	0.61	0.47	0.80
basophil	166	0.64	0.65	0.90	0.41	0.00	0.66	0.64	0.73	0.82
tissue-resident macrophage	136	0.67	0.04	0.84	0.27	0.00	0.31	0.53	0.50	0.77
non-classical monocyte	113	0.29	0.48	0.46	0.31	0.00	0.20	0.24	0.34	0.54
activated CD8-positive, alpha-beta T cell	113	0.34	0.33	0.31	0.03	0.00	0.09	0.27	0.30	0.42
naive thymus-derived CD8-positive, alpha-beta T cell	112	0.13	0.02	0.45	0.14	0.00	0.15	0.11	0.15	0.24
myeloid leukocyte	96	0.26	0.40	0.61	0.16	0.00	0.17	0.23	0.21	0.60
erythroid progenitor cell	106	0.67	0.70	0.69	0.58	0.00	0.63	0.66	0.70	0.72
innate lymphoid cell	84	0.21	0.31	0.31	0.25	0.00	0.29	0.26	0.23	0.37
hematopoietic stem cell	72	0.72	0.78	0.78	0.69	0.00	0.68	0.76	0.76	0.80
granulocyte	69	0.22	0.26	0.61	0.45	0.00	0.09	0.27	0.26	0.48
CD8-positive, alpha-beta thymocyte	70	0.49	0.62	0.58	0.54	0.00	0.54	0.26	0.42	0.72
activated CD4-positive, alpha-beta T cell	60	0.05	0.09	0.15	0.03	0.00	0.12	0.10	0.12	0.20
myeloid dendritic cell	46	0.11	0.36	0.41	0.18	0.00	0.11	0.13	0.14	0.21
platelet	53	0.68	0.96	0.98	0.94	0.00	0.86	0.81	0.75	0.96
common myeloid progenitor	39	0.60	0.70	0.73	0.32	0.00	0.41	0.58	0.77	0.73
thymocyte	43	0.00	0.46	0.44	0.60	0.00	0.55	0.22	0.47	0.79
microglial cell	39	0.08	0.00	0.38	0.08	0.00	0.10	0.15	0.17	0.21
colon macrophage	41	0.31	0.52	0.77	0.18	0.00	0.06	0.23	0.34	0.72
leukocyte	15	0.15	0.32	0.09	0.11	0.00	0.05	0.07	0.15	0.26
plasmacytoid dendritic cell	7	0.00	0.43	0.43	0.15	0.00	0.08	0.29	0.28	0.44
hematopoietic cell	8	0.94	0.88	0.86	0.80	0.00	0.07	0.94	0.52	0.80
myeloid cell	2	0.00	0.00	0.00	0.00	0.00	0.00	0.13	0.00	0.00
Langerhans cell	7	0.37	0.71	0.55	0.31	0.00	0.05	0.35	0.32	0.67
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 on bbknn	knn on harmony	knn on scvi	onclass	scanvi	svm	xgboost	Consensus Prediction
B cell	103201	0.99	0.99	0.99	0.99	0.00	0.98	0.99	0.99	0.99
CD4-positive, alpha-beta T cell	87384	0.56	0.82	0.87	0.82	0.00	0.42	0.43	0.59	0.82
CD8-positive, alpha-beta T cell	68583	0.68	0.81	0.87	0.81	0.00	0.70	0.55	0.65	0.82
neutrophil	62542	0.95	0.98	0.98	0.98	0.00	0.91	0.95	0.95	0.98
macrophage	62204	0.81	0.87	0.95	0.88	0.00	0.80	0.72	0.75	0.92
plasma cell	24554	0.98	0.99	0.98	0.98	0.00	0.98	0.99	0.98	0.99
monocyte	23139	0.58	0.54	0.85	0.68	0.00	0.59	0.48	0.56	0.75
classical monocyte	16393	0.65	0.66	0.84	0.71	0.00	0.67	0.58	0.68	0.79
erythrocyte	13112	0.98	0.97	0.98	0.99	0.00	0.98	0.97	0.97	0.98
natural killer cell	12819	0.72	0.76	0.84	0.80	0.00	0.73	0.70	0.74	0.78
naive thymus-derived CD4-positive, alpha-beta T cell	8825	0.24	0.10	0.47	0.19	0.00	0.23	0.24	0.32	0.38
T cell	5680	0.43	0.54	0.70	0.35	0.00	0.33	0.35	0.47	0.59
mast cell	5640	0.87	0.87	0.97	0.92	0.00	0.95	0.91	0.91	0.95
intermediate monocyte	4927	0.35	0.22	0.69	0.49	0.00	0.38	0.34	0.44	0.57
mature NK T cell	4854	0.55	0.55	0.74	0.60	0.00	0.54	0.41	0.50	0.64
mononuclear phagocyte	4782	0.50	0.01	0.93	0.46	0.00	0.77	0.57	0.55	0.89
CD4-positive, alpha-beta thymocyte	4224	0.38	0.37	0.74	0.50	0.00	0.53	0.37	0.45	0.67
regulatory T cell	2356	0.28	0.15	0.57	0.29	0.00	0.24	0.26	0.37	0.48
hematopoietic precursor cell	1931	0.53	0.74	0.86	0.79	0.00	0.51	0.57	0.60	0.76
gamma-delta T cell	1783	0.45	0.76	0.84	0.51	0.00	0.69	0.64	0.50	0.81
basophil	1503	0.63	0.49	0.95	0.77	0.00	0.88	0.67	0.77	0.89
tissue-resident macrophage	1219	0.70	0.01	0.90	0.65	0.00	0.57	0.56	0.54	0.79
non-classical monocyte	1171	0.27	0.41	0.58	0.53	0.00	0.26	0.30	0.42	0.60
activated CD8-positive, alpha-beta T cell	1029	0.37	0.27	0.46	0.18	0.00	0.41	0.30	0.31	0.69
naive thymus-derived CD8-positive, alpha-beta T cell	944	0.14	0.01	0.61	0.32	0.00	0.18	0.13	0.15	0.31
myeloid leukocyte	898	0.27	0.24	0.74	0.37	0.00	0.59	0.28	0.26	0.77
erythroid progenitor cell	865	0.66	0.63	0.82	0.78	0.00	0.75	0.76	0.74	0.80
innate lymphoid cell	887	0.21	0.29	0.58	0.47	0.00	0.50	0.32	0.28	0.47
hematopoietic stem cell	786	0.71	0.78	0.88	0.81	0.00	0.79	0.81	0.86	0.87
granulocyte	700	0.25	0.21	0.73	0.61	0.00	0.14	0.30	0.30	0.59
CD8-positive, alpha-beta thymocyte	661	0.40	0.53	0.64	0.54	0.00	0.61	0.30	0.46	0.78
activated CD4-positive, alpha-beta T cell	512	0.05	0.03	0.50	0.20	0.00	0.20	0.12	0.14	0.32
myeloid dendritic cell	524	0.13	0.26	0.60	0.43	0.00	0.17	0.19	0.25	0.31
platelet	441	0.74	0.94	0.97	0.97	0.00	0.82	0.87	0.80	0.97
common myeloid progenitor	417	0.58	0.58	0.83	0.73	0.00	0.77	0.81	0.89	0.88
thymocyte	412	0.00	0.41	0.55	0.51	0.00	0.56	0.25	0.59	0.90
microglial cell	353	0.12	0.16	0.64	0.25	0.00	0.28	0.21	0.21	0.42
colon macrophage	286	0.24	0.27	0.85	0.38	0.00	0.41	0.26	0.34	0.80
leukocyte	171	0.11	0.06	0.48	0.16	0.00	0.20	0.16	0.17	0.35
plasmacytoid dendritic cell	91	0.00	0.54	0.77	0.63	0.00	0.15	0.67	0.52	0.75
hematopoietic cell	90	0.87	0.74	0.96	0.79	0.00	0.07	0.95	0.62	0.80
myeloid cell	79	0.00	0.00	0.54	0.09	0.00	0.42	0.41	0.30	0.91
Langerhans cell	69	0.34	0.38	0.80	0.53	0.00	0.10	0.31	0.32	0.55
T follicular helper cell	6	0.00	0.00	0.00	0.00	0.00	0.02	0.92	0.55	0.80
erythroid lineage cell	2	0.00	0.00	0.00	0.00	0.00	0.12	1.00	0.80	0.67

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