popV/tabula_sapiens_Muscle

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
mesenchymal stem cell	2337	0.98	0.98	0.99	0.98	0.00	0.92	0.97	0.97	0.99
skeletal muscle satellite stem cell	614	0.97	0.98	0.97	0.98	0.00	0.96	0.97	0.98	0.98
endothelial cell	360	0.94	0.95	0.93	0.92	0.00	0.95	0.94	0.94	0.95
capillary endothelial cell	331	0.88	0.92	0.92	0.91	0.00	0.90	0.87	0.89	0.92
macrophage	279	0.95	0.97	0.97	0.95	0.00	0.91	0.94	0.95	0.96
pericyte	239	0.88	0.89	0.90	0.90	0.00	0.84	0.88	0.90	0.91
CD8-positive, alpha-beta T cell	145	0.78	0.77	0.79	0.75	0.00	0.66	0.71	0.81	0.81
endothelial cell of vascular tree	71	0.83	0.90	0.79	0.74	0.00	0.85	0.84	0.81	0.88
CD4-positive, alpha-beta T cell	50	0.53	0.48	0.42	0.26	0.00	0.41	0.44	0.60	0.54
fast muscle cell	53	0.87	0.89	0.87	0.79	0.00	0.89	0.89	0.89	0.89
tendon cell	37	0.74	0.80	0.82	0.70	0.00	0.33	0.52	0.50	0.80
smooth muscle cell	20	0.33	0.42	0.17	0.46	0.00	0.45	0.65	0.61	0.62
endothelial cell of artery	21	0.91	0.89	0.83	0.73	0.00	0.61	0.82	0.80	0.90
slow muscle cell	17	0.76	0.78	0.78	0.10	0.00	0.74	0.82	0.78	0.80
neutrophil	23	0.75	0.80	0.81	0.77	0.00	0.74	0.76	0.78	0.74
endothelial cell of lymphatic vessel	9	0.82	0.82	0.82	0.67	0.00	0.60	0.89	0.74	0.82
erythrocyte	12	0.43	0.30	0.92	0.47	0.00	0.55	0.65	0.58	0.85
T cell	15	0.00	0.12	0.24	0.00	0.00	0.06	0.33	0.53	0.12
mature NK T cell	6	0.29	0.00	0.00	0.00	0.00	0.36	0.31	0.43	0.36
granulocyte	6	0.60	0.00	0.56	0.67	0.00	0.44	0.53	0.62	0.67
natural killer cell	4	0.25	0.44	0.57	0.40	0.00	0.13	0.80	0.50	0.25
mast cell	4	0.42	0.57	0.47	0.44	0.00	0.50	0.57	0.57	0.50
epithelial cell	8	0.57	0.50	0.57	0.36	0.00	0.31	0.53	0.62	0.57
B cell	8	0.62	0.77	0.67	0.50	0.00	0.67	0.93	0.93	0.77
monocyte	4	0.00	0.00	0.00	0.00	0.00	0.24	0.33	0.20	0.00
basophil	3	0.00	0.00	0.00	0.00	0.00	0.29	0.00	0.80	0.00
myeloid dendritic cell	2	0.00	0.00	0.00	0.00	0.00	0.20	0.00	0.40	0.00
plasma cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
non-classical monocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
intermediate monocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
mesenchymal cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
mesothelial 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
mesenchymal stem cell	21143	0.98	0.98	0.99	0.98	0.00	0.92	0.97	0.97	0.99
skeletal muscle satellite stem cell	5536	0.98	0.98	0.98	0.98	0.00	0.96	0.98	0.98	0.98
endothelial cell	3166	0.92	0.94	0.93	0.91	0.00	0.94	0.94	0.95	0.95
capillary endothelial cell	2959	0.88	0.91	0.92	0.90	0.00	0.89	0.91	0.91	0.92
macrophage	2450	0.96	0.96	0.96	0.96	0.00	0.93	0.97	0.96	0.97
pericyte	2147	0.89	0.91	0.91	0.92	0.00	0.91	0.92	0.93	0.94
CD8-positive, alpha-beta T cell	1272	0.74	0.78	0.82	0.77	0.00	0.76	0.85	0.89	0.88
endothelial cell of vascular tree	652	0.85	0.90	0.85	0.73	0.00	0.89	0.89	0.90	0.92
CD4-positive, alpha-beta T cell	464	0.50	0.54	0.57	0.41	0.00	0.63	0.78	0.83	0.74
fast muscle cell	421	0.95	0.95	0.94	0.86	0.00	0.90	0.94	0.96	0.96
tendon cell	383	0.74	0.81	0.82	0.68	0.00	0.38	0.60	0.57	0.79
smooth muscle cell	198	0.44	0.56	0.21	0.64	0.00	0.71	0.81	0.80	0.89
endothelial cell of artery	159	0.74	0.85	0.84	0.76	0.00	0.61	0.86	0.87	0.87
slow muscle cell	157	0.91	0.93	0.91	0.62	0.00	0.87	0.97	0.98	0.96
neutrophil	151	0.75	0.79	0.82	0.77	0.00	0.91	0.93	0.94	0.93
endothelial cell of lymphatic vessel	146	0.90	0.91	0.91	0.89	0.00	0.91	0.93	0.93	0.94
erythrocyte	112	0.45	0.30	0.89	0.54	0.00	0.52	0.69	0.65	0.83
T cell	93	0.00	0.10	0.16	0.13	0.00	0.37	0.92	0.88	0.81
mature NK T cell	92	0.42	0.14	0.38	0.10	0.00	0.51	0.78	0.84	0.82
granulocyte	88	0.71	0.07	0.69	0.70	0.00	0.67	0.85	0.94	0.95
natural killer cell	87	0.59	0.51	0.31	0.24	0.00	0.36	0.90	0.89	0.82
mast cell	62	0.69	0.71	0.72	0.74	0.00	0.81	0.96	0.93	0.78
epithelial cell	49	0.67	0.51	0.66	0.52	0.00	0.62	0.88	0.92	0.72
B cell	41	0.77	0.91	0.89	0.78	0.00	0.83	0.99	1.00	0.96
monocyte	28	0.00	0.07	0.00	0.00	0.00	0.34	0.70	0.73	0.19
basophil	8	0.00	0.00	0.00	0.00	0.00	0.61	1.00	0.94	0.00
myeloid dendritic cell	7	0.00	0.00	0.00	0.00	0.00	0.19	0.74	0.70	0.00
plasma cell	4	0.00	0.00	0.00	0.00	0.00	0.80	0.89	0.89	0.86
non-classical monocyte	3	0.00	0.00	0.00	0.00	0.00	0.24	1.00	1.00	0.00
intermediate monocyte	3	0.00	0.00	0.00	0.00	0.00	0.40	1.00	1.00	0.00
mesenchymal cell	2	0.00	0.00	0.00	0.00	0.00	0.00	0.80	0.50	0.00
mesothelial cell	1	0.00	0.00	0.00	0.00	0.00	0.11	1.00	1.00	1.00

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