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	11277	0.99	0.99	0.98	0.98	0.00	0.99	0.97	0.98	0.99
CD4-positive, alpha-beta T cell	9719	0.49	0.80	0.79	0.73	0.00	0.60	0.37	0.49	0.78
CD8-positive, alpha-beta T cell	7653	0.68	0.79	0.76	0.70	0.00	0.72	0.48	0.65	0.79
neutrophil	7010	0.96	0.98	0.96	0.97	0.00	0.95	0.92	0.94	0.98
macrophage	6802	0.83	0.87	0.88	0.81	0.00	0.77	0.72	0.75	0.89
plasma cell	2783	0.98	0.98	0.97	0.98	0.00	0.97	0.97	0.98	0.99
monocyte	2615	0.32	0.57	0.71	0.39	0.00	0.24	0.40	0.55	0.54
classical monocyte	1805	0.61	0.66	0.69	0.44	0.00	0.55	0.51	0.66	0.68
erythrocyte	1501	0.97	0.98	0.97	0.97	0.00	0.96	0.96	0.96	0.97
natural killer cell	1416	0.69	0.73	0.72	0.59	0.00	0.64	0.59	0.68	0.73
naive thymus-derived CD4-positive, alpha-beta T cell	997	0.20	0.04	0.25	0.05	0.00	0.19	0.19	0.25	0.20
T cell	603	0.38	0.41	0.46	0.09	0.00	0.25	0.29	0.38	0.48
mast cell	591	0.86	0.91	0.91	0.80	0.00	0.81	0.85	0.91	0.94
intermediate monocyte	546	0.31	0.26	0.45	0.10	0.00	0.20	0.29	0.42	0.47
mature NK T cell	546	0.51	0.51	0.55	0.21	0.00	0.40	0.33	0.46	0.58
mononuclear phagocyte	554	0.66	0.01	0.56	0.11	0.00	0.01	0.59	0.56	0.50
CD4-positive, alpha-beta thymocyte	458	0.38	0.31	0.44	0.06	0.00	0.16	0.30	0.43	0.47
regulatory T cell	297	0.23	0.14	0.18	0.04	0.00	0.14	0.16	0.21	0.32
hematopoietic precursor cell	204	0.49	0.73	0.76	0.58	0.00	0.42	0.46	0.54	0.66
gamma-delta T cell	191	0.64	0.78	0.66	0.02	0.00	0.24	0.43	0.48	0.77
basophil	170	0.60	0.72	0.66	0.26	0.00	0.50	0.67	0.80	0.85
tissue-resident macrophage	136	0.62	0.00	0.70	0.25	0.00	0.30	0.43	0.49	0.65
non-classical monocyte	113	0.21	0.34	0.36	0.02	0.00	0.29	0.22	0.31	0.46
activated CD8-positive, alpha-beta T cell	123	0.29	0.24	0.29	0.05	0.00	0.09	0.23	0.32	0.45
naive thymus-derived CD8-positive, alpha-beta T cell	112	0.12	0.02	0.30	0.02	0.00	0.12	0.12	0.17	0.27
myeloid leukocyte	90	0.17	0.53	0.59	0.04	0.00	0.12	0.20	0.23	0.53
erythroid progenitor cell	104	0.66	0.75	0.63	0.57	0.00	0.58	0.62	0.66	0.73
innate lymphoid cell	85	0.20	0.29	0.30	0.23	0.00	0.30	0.16	0.24	0.33
hematopoietic stem cell	72	0.71	0.74	0.75	0.59	0.00	0.46	0.68	0.73	0.77
granulocyte	74	0.39	0.30	0.50	0.21	0.00	0.19	0.20	0.24	0.60
CD8-positive, alpha-beta thymocyte	66	0.42	0.28	0.23	0.12	0.00	0.23	0.14	0.26	0.46
activated CD4-positive, alpha-beta T cell	65	0.08	0.06	0.09	0.00	0.00	0.12	0.10	0.18	0.22
myeloid dendritic cell	47	0.16	0.32	0.34	0.04	0.00	0.15	0.10	0.15	0.21
platelet	49	0.62	0.95	0.98	0.92	0.00	0.33	0.77	0.69	0.87
common myeloid progenitor	42	0.58	0.73	0.67	0.27	0.00	0.59	0.60	0.71	0.76
thymocyte	48	0.00	0.17	0.28	0.15	0.00	0.37	0.15	0.43	0.57
microglial cell	39	0.13	0.05	0.32	0.09	0.00	0.08	0.17	0.17	0.26
colon macrophage	41	0.35	0.42	0.69	0.00	0.00	0.07	0.25	0.40	0.64
leukocyte	16	0.09	0.29	0.11	0.00	0.00	0.05	0.03	0.14	0.14
plasmacytoid dendritic cell	8	0.50	0.36	0.53	0.15	0.00	0.06	0.18	0.31	0.50
hematopoietic cell	8	0.88	0.80	0.67	0.40	0.00	0.18	1.00	0.44	0.84
myeloid cell	2	0.00	0.00	0.00	0.00	0.00	0.00	0.07	0.13	0.67
Langerhans cell	6	0.00	0.22	0.67	0.00	0.00	0.21	0.30	0.32	0.80
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	103204	0.99	0.99	0.98	0.98	0.00	0.98	0.97	0.98	0.99
CD4-positive, alpha-beta T cell	87396	0.48	0.79	0.84	0.79	0.00	0.59	0.38	0.50	0.80
CD8-positive, alpha-beta T cell	68604	0.68	0.78	0.83	0.77	0.00	0.70	0.49	0.65	0.81
neutrophil	62514	0.96	0.97	0.97	0.95	0.00	0.95	0.93	0.94	0.98
macrophage	62221	0.83	0.86	0.92	0.84	0.00	0.81	0.71	0.76	0.91
plasma cell	24561	0.98	0.98	0.98	0.98	0.00	0.97	0.97	0.98	0.99
monocyte	23134	0.32	0.51	0.81	0.59	0.00	0.54	0.42	0.55	0.68
classical monocyte	16394	0.62	0.64	0.81	0.65	0.00	0.70	0.52	0.67	0.75
erythrocyte	13107	0.96	0.97	0.98	0.98	0.00	0.95	0.96	0.96	0.97
natural killer cell	12814	0.70	0.73	0.81	0.71	0.00	0.70	0.61	0.69	0.76
naive thymus-derived CD4-positive, alpha-beta T cell	8830	0.20	0.06	0.40	0.18	0.00	0.32	0.21	0.26	0.33
T cell	5685	0.40	0.40	0.62	0.29	0.00	0.44	0.32	0.40	0.58
mast cell	5626	0.85	0.89	0.94	0.89	0.00	0.91	0.88	0.92	0.95
intermediate monocyte	4931	0.32	0.20	0.63	0.35	0.00	0.30	0.32	0.43	0.53
mature NK T cell	4845	0.52	0.47	0.66	0.39	0.00	0.49	0.35	0.48	0.62
mononuclear phagocyte	4782	0.64	0.00	0.83	0.35	0.00	0.88	0.58	0.56	0.89
CD4-positive, alpha-beta thymocyte	4227	0.39	0.27	0.60	0.18	0.00	0.63	0.35	0.45	0.64
regulatory T cell	2352	0.20	0.09	0.36	0.11	0.00	0.15	0.18	0.22	0.38
hematopoietic precursor cell	1936	0.52	0.71	0.82	0.68	0.00	0.48	0.50	0.57	0.72
gamma-delta T cell	1784	0.63	0.74	0.77	0.13	0.00	0.47	0.46	0.48	0.78
basophil	1499	0.51	0.63	0.82	0.70	0.00	0.85	0.70	0.81	0.89
tissue-resident macrophage	1219	0.62	0.01	0.83	0.48	0.00	0.53	0.45	0.50	0.74
non-classical monocyte	1171	0.23	0.32	0.47	0.19	0.00	0.33	0.27	0.37	0.53
activated CD8-positive, alpha-beta T cell	1024	0.28	0.12	0.30	0.13	0.00	0.60	0.25	0.33	0.66
naive thymus-derived CD8-positive, alpha-beta T cell	944	0.13	0.01	0.53	0.04	0.00	0.28	0.14	0.18	0.51
myeloid leukocyte	904	0.17	0.33	0.68	0.24	0.00	0.56	0.29	0.30	0.64
erythroid progenitor cell	867	0.63	0.62	0.78	0.75	0.00	0.66	0.72	0.73	0.77
innate lymphoid cell	886	0.22	0.25	0.50	0.36	0.00	0.64	0.24	0.30	0.50
hematopoietic stem cell	786	0.72	0.76	0.84	0.73	0.00	0.65	0.81	0.87	0.85
granulocyte	695	0.37	0.21	0.64	0.52	0.00	0.39	0.25	0.27	0.72
CD8-positive, alpha-beta thymocyte	665	0.37	0.28	0.33	0.14	0.00	0.44	0.23	0.37	0.68
activated CD4-positive, alpha-beta T cell	507	0.06	0.02	0.29	0.20	0.00	0.19	0.13	0.18	0.28
myeloid dendritic cell	523	0.16	0.23	0.53	0.23	0.00	0.27	0.16	0.23	0.34
platelet	445	0.68	0.89	0.95	0.94	0.00	0.33	0.83	0.80	0.91
common myeloid progenitor	414	0.56	0.57	0.76	0.69	0.00	0.74	0.76	0.90	0.87
thymocyte	407	0.00	0.20	0.35	0.16	0.00	0.61	0.21	0.59	0.85
microglial cell	353	0.13	0.04	0.51	0.10	0.00	0.56	0.23	0.23	0.49
colon macrophage	286	0.28	0.23	0.78	0.21	0.00	0.49	0.28	0.37	0.72
leukocyte	170	0.05	0.04	0.36	0.18	0.00	0.37	0.10	0.19	0.37
plasmacytoid dendritic cell	90	0.56	0.50	0.75	0.53	0.00	0.13	0.30	0.48	0.67
hematopoietic cell	90	0.79	0.73	0.92	0.63	0.00	0.30	0.96	0.58	0.85
myeloid cell	79	0.00	0.00	0.31	0.05	0.00	0.45	0.28	0.37	0.83
Langerhans cell	70	0.00	0.43	0.74	0.38	0.00	0.18	0.33	0.35	0.73
T follicular helper cell	6	0.00	0.00	0.00	0.00	0.00	0.12	0.46	0.35	0.91
erythroid lineage cell	2	0.00	0.00	0.00	0.00	0.00	0.01	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