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	15921	0.99	0.99	0.97	0.99	0.00	0.98	0.99	0.99	1.00
CD4-positive, alpha-beta T cell	10228	0.40	0.81	0.80	0.79	0.00	0.42	0.34	0.51	0.75
CD8-positive, alpha-beta T cell	8293	0.75	0.81	0.82	0.78	0.00	0.71	0.58	0.68	0.82
neutrophil	17440	0.99	1.00	0.96	1.00	0.00	0.94	0.97	0.97	0.99
macrophage	12654	0.93	0.93	0.92	0.90	0.00	0.87	0.87	0.88	0.95
plasma cell	6650	0.98	0.99	0.87	0.98	0.00	0.98	0.98	0.98	0.99
monocyte	7170	0.03	0.24	0.79	0.29	0.00	0.18	0.28	0.27	0.18
classical monocyte	3217	0.39	0.47	0.62	0.39	0.00	0.37	0.31	0.36	0.42
erythrocyte	1496	0.98	0.99	0.85	0.99	0.00	0.97	0.96	0.98	0.98
natural killer cell	1805	0.65	0.74	0.77	0.71	0.00	0.68	0.64	0.70	0.73
naive thymus-derived CD4-positive, alpha-beta T cell	1264	0.15	0.06	0.35	0.02	0.00	0.25	0.19	0.29	0.23
T cell	476	0.41	0.38	0.66	0.44	0.00	0.33	0.27	0.45	0.51
mast cell	383	0.48	0.55	0.82	0.54	0.00	0.79	0.76	0.66	0.71
intermediate monocyte	379	0.07	0.15	0.36	0.09	0.00	0.05	0.06	0.08	0.09
mature NK T cell	1096	0.64	0.65	0.60	0.54	0.00	0.57	0.49	0.56	0.67
mononuclear phagocyte	62	0.00	0.00	0.00	0.00	0.00	0.00	0.04	0.05	0.00
CD4-positive, alpha-beta thymocyte	5	0.00	0.00	0.00	0.00	0.00	0.01	0.00	0.00	0.00
regulatory T cell	536	0.34	0.00	0.22	0.03	0.00	0.33	0.35	0.55	0.49
hematopoietic precursor cell	125	0.23	0.53	0.55	0.46	0.00	0.22	0.24	0.27	0.40
gamma-delta T cell	517	0.83	0.27	0.72	0.26	0.00	0.32	0.75	0.73	0.81
basophil	584	0.15	0.03	0.91	0.09	0.00	0.81	0.75	0.75	0.71
tissue-resident macrophage	18	0.73	0.00	0.05	0.04	0.00	0.03	0.26	0.16	0.27
non-classical monocyte	214	0.31	0.45	0.39	0.33	0.00	0.15	0.21	0.27	0.44
activated CD8-positive, alpha-beta T cell	9	0.11	0.00	0.00	0.00	0.00	0.00	0.02	0.03	0.13
naive thymus-derived CD8-positive, alpha-beta T cell	86	0.13	0.00	0.18	0.02	0.00	0.16	0.07	0.08	0.24
myeloid leukocyte	237	0.49	0.02	0.40	0.02	0.00	0.08	0.28	0.29	0.40
erythroid progenitor cell	81	0.61	0.74	0.70	0.67	0.00	0.48	0.71	0.72	0.71
innate lymphoid cell	209	0.36	0.15	0.26	0.08	0.00	0.19	0.29	0.41	0.43
hematopoietic stem cell	51	0.62	0.59	0.64	0.59	0.00	0.47	0.53	0.63	0.65
granulocyte	20	0.09	0.00	0.00	0.00	0.00	0.01	0.01	0.03	0.00
CD8-positive, alpha-beta thymocyte	4	0.00	0.00	0.00	0.00	0.00	0.00	0.02	0.05	0.00
activated CD4-positive, alpha-beta T cell	4	0.01	0.00	0.00	0.00	0.00	0.00	0.00	0.01	0.01
myeloid dendritic cell	70	0.16	0.14	0.34	0.05	0.00	0.11	0.14	0.13	0.18
platelet	131	0.76	0.92	0.84	0.96	0.00	0.68	0.71	0.76	0.85
common myeloid progenitor	5	0.00	0.12	0.07	0.10	0.00	0.04	0.00	0.15	0.07
thymocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
microglial cell	89	0.50	0.00	0.04	0.00	0.00	0.33	0.40	0.36	0.42
colon macrophage	118	0.21	0.00	0.73	0.00	0.00	0.00	0.29	0.40	0.65
leukocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
hematopoietic cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
plasmacytoid dendritic cell	31	0.92	0.44	0.36	0.17	0.00	0.12	0.58	0.57	0.81
myeloid cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
Langerhans cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
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	98572	0.99	0.99	0.99	0.99	0.00	0.98	0.98	0.99	0.99
CD4-positive, alpha-beta T cell	86890	0.58	0.81	0.85	0.80	0.00	0.56	0.41	0.59	0.81
CD8-positive, alpha-beta T cell	67971	0.68	0.80	0.84	0.79	0.00	0.69	0.54	0.65	0.81
neutrophil	52085	0.96	0.98	0.98	0.98	0.00	0.95	0.95	0.95	0.98
macrophage	56393	0.82	0.84	0.92	0.86	0.00	0.81	0.70	0.74	0.91
plasma cell	20697	0.96	0.98	0.98	0.99	0.00	0.98	0.96	0.98	0.99
monocyte	18581	0.48	0.47	0.79	0.59	0.00	0.49	0.45	0.56	0.67
classical monocyte	14982	0.66	0.70	0.83	0.71	0.00	0.71	0.64	0.74	0.79
erythrocyte	13115	0.97	0.97	0.97	0.98	0.00	0.96	0.96	0.97	0.98
natural killer cell	12426	0.70	0.77	0.81	0.77	0.00	0.74	0.69	0.74	0.77
naive thymus-derived CD4-positive, alpha-beta T cell	8563	0.23	0.11	0.34	0.04	0.00	0.29	0.23	0.32	0.32
T cell	5814	0.42	0.37	0.64	0.25	0.00	0.39	0.36	0.45	0.59
mast cell	5835	0.87	0.89	0.96	0.91	0.00	0.96	0.90	0.92	0.95
intermediate monocyte	5099	0.36	0.21	0.64	0.38	0.00	0.34	0.38	0.49	0.57
mature NK T cell	4298	0.50	0.52	0.67	0.49	0.00	0.53	0.39	0.49	0.63
mononuclear phagocyte	5274	0.70	0.00	0.91	0.39	0.00	0.86	0.63	0.63	0.89
CD4-positive, alpha-beta thymocyte	4680	0.41	0.02	0.68	0.36	0.00	0.62	0.39	0.50	0.69
regulatory T cell	2112	0.23	0.05	0.45	0.05	0.00	0.24	0.25	0.34	0.46
hematopoietic precursor cell	2015	0.52	0.69	0.81	0.76	0.00	0.55	0.60	0.63	0.74
gamma-delta T cell	1460	0.45	0.34	0.77	0.29	0.00	0.41	0.44	0.43	0.76
basophil	1085	0.54	0.06	0.92	0.50	0.00	0.82	0.64	0.70	0.86
tissue-resident macrophage	1337	0.64	0.00	0.86	0.56	0.00	0.68	0.53	0.57	0.77
non-classical monocyte	1070	0.22	0.37	0.46	0.32	0.00	0.24	0.34	0.41	0.56
activated CD8-positive, alpha-beta T cell	1138	0.35	0.03	0.28	0.13	0.00	0.57	0.26	0.35	0.62
naive thymus-derived CD8-positive, alpha-beta T cell	970	0.13	0.00	0.53	0.11	0.00	0.21	0.15	0.18	0.34
myeloid leukocyte	762	0.15	0.00	0.64	0.03	0.00	0.58	0.24	0.24	0.67
erythroid progenitor cell	890	0.59	0.63	0.81	0.71	0.00	0.63	0.76	0.74	0.76
innate lymphoid cell	762	0.21	0.20	0.49	0.32	0.00	0.51	0.22	0.26	0.46
hematopoietic stem cell	807	0.68	0.78	0.83	0.78	0.00	0.71	0.79	0.85	0.86
granulocyte	749	0.13	0.02	0.72	0.53	0.00	0.30	0.39	0.38	0.77
CD8-positive, alpha-beta thymocyte	727	0.42	0.08	0.42	0.19	0.00	0.64	0.35	0.44	0.69
activated CD4-positive, alpha-beta T cell	568	0.04	0.00	0.40	0.04	0.00	0.17	0.13	0.15	0.32
myeloid dendritic cell	500	0.11	0.18	0.48	0.25	0.00	0.20	0.21	0.25	0.36
platelet	363	0.72	0.87	0.92	0.94	0.00	0.59	0.77	0.81	0.90
common myeloid progenitor	451	0.00	0.63	0.78	0.70	0.00	0.77	0.81	0.91	0.88
thymocyte	455	0.00	0.02	0.42	0.23	0.00	0.36	0.27	0.59	0.91
microglial cell	315	0.11	0.04	0.42	0.04	0.00	0.44	0.23	0.23	0.45
colon macrophage	209	0.27	0.01	0.72	0.00	0.00	0.52	0.26	0.39	0.83
leukocyte	187	0.09	0.01	0.34	0.01	0.00	0.16	0.16	0.20	0.43
hematopoietic cell	100	0.00	0.04	0.93	0.69	0.00	0.12	0.48	0.58	0.79
plasmacytoid dendritic cell	68	0.28	0.49	0.55	0.38	0.00	0.05	0.38	0.49	0.67
myeloid cell	81	0.00	0.00	0.22	0.00	0.00	0.31	0.18	0.40	0.84
Langerhans cell	76	0.27	0.27	0.73	0.53	0.00	0.10	0.25	0.31	0.51
T follicular helper cell	6	0.00	0.00	0.00	0.00	0.00	0.08	0.10	0.71	0.73
erythroid lineage cell	2	0.00	0.00	0.00	0.00	0.00	0.00	0.00	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