popV/tabula_sapiens_Stromal

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
fibroblast	8306	0.82	0.87	0.89	0.68	0.00	0.66	0.72	0.75	0.89
stromal cell of ovary	3508	0.98	0.97	0.91	0.62	0.00	0.63	0.97	0.97	0.99
mesenchymal stem cell	2264	0.93	0.92	0.89	0.46	0.00	0.44	0.89	0.90	0.96
smooth muscle cell	1820	0.79	0.80	0.85	0.71	0.00	0.64	0.78	0.81	0.86
pericyte	1095	0.72	0.76	0.82	0.64	0.00	0.53	0.69	0.73	0.80
skeletal muscle satellite stem cell	668	0.95	0.96	0.96	0.80	0.00	0.82	0.96	0.94	0.97
blood vessel smooth muscle cell	582	0.87	0.83	0.94	0.64	0.00	0.65	0.87	0.86	0.95
regular atrial cardiac myocyte	621	0.74	0.82	0.77	0.26	0.00	0.38	0.85	0.83	0.86
fibroblast of breast	541	0.98	0.22	0.73	0.14	0.00	0.00	0.96	0.82	0.89
vascular associated smooth muscle cell	471	0.72	0.52	0.63	0.40	0.00	0.22	0.64	0.69	0.76
myofibroblast cell	422	0.62	0.80	0.82	0.42	0.00	0.42	0.58	0.64	0.80
thymic fibroblast type 2	404	0.68	0.23	0.43	0.07	0.00	0.15	0.61	0.65	0.55
mesenchymal stem cell of adipose tissue	361	0.34	0.07	0.67	0.35	0.00	0.30	0.38	0.39	0.51
stromal cell	298	0.88	0.64	0.50	0.15	0.00	0.40	0.80	0.85	0.93
thymic fibroblast type 1	334	0.67	0.39	0.64	0.11	0.00	0.03	0.55	0.53	0.64
ventricular cardiac muscle cell	247	0.42	0.24	0.61	0.42	0.00	0.50	0.69	0.67	0.71
fibroblast of cardiac tissue	193	0.70	0.95	0.94	0.11	0.00	0.05	0.76	0.76	0.95
alveolar adventitial fibroblast	123	0.79	0.82	0.67	0.28	0.00	0.09	0.62	0.80	0.83
adventitial cell	106	0.24	0.25	0.15	0.01	0.00	0.15	0.31	0.38	0.46
theca cell	120	0.71	0.81	0.88	0.60	0.00	0.72	0.83	0.76	0.88
keratocyte	92	0.47	0.37	0.46	0.02	0.00	0.13	0.47	0.42	0.57
myometrial cell	102	0.89	0.46	0.90	0.52	0.00	0.67	0.73	0.76	0.90
mural cell	61	0.47	0.76	0.69	0.20	0.00	0.29	0.52	0.59	0.80
Mueller cell	50	0.98	0.98	0.98	0.81	0.00	0.80	0.96	0.90	0.98
fast muscle cell	54	0.38	0.73	0.78	0.71	0.00	0.77	0.85	0.86	0.87
pancreatic stellate cell	37	0.69	0.00	0.51	0.11	0.00	0.05	0.68	0.75	0.74
tendon cell	40	0.42	0.57	0.48	0.21	0.00	0.24	0.39	0.37	0.67
muscle cell	34	0.71	0.33	0.68	0.60	0.00	0.72	0.97	0.93	0.94
Schwann cell	34	0.76	0.83	0.89	0.82	0.00	0.39	0.79	0.70	0.91
melanocyte	16	0.00	0.68	0.91	0.67	0.00	0.11	0.86	0.81	0.91
hepatic stellate cell	29	0.52	0.12	0.64	0.21	0.00	0.13	0.75	0.81	0.68
bronchial smooth muscle cell	15	0.30	0.39	0.09	0.08	0.00	0.14	0.32	0.32	0.46
tongue muscle cell	17	0.58	0.64	0.67	0.10	0.00	0.59	0.73	0.55	0.62
slow muscle cell	14	0.60	0.87	0.51	0.29	0.00	0.76	0.87	0.87	0.87
connective tissue cell	10	0.00	0.00	0.00	0.00	0.00	0.00	0.13	0.12	0.13
adipocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
glial cell	1	0.00	0.00	0.67	0.00	0.00	0.02	0.20	0.10	0.18
Leydig cell	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

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
fibroblast	74870	0.82	0.86	0.93	0.76	0.00	0.85	0.72	0.75	0.92
stromal cell of ovary	31495	0.98	0.96	0.93	0.69	0.00	0.94	0.97	0.97	0.99
mesenchymal stem cell	21232	0.93	0.91	0.94	0.55	0.00	0.94	0.90	0.90	0.97
smooth muscle cell	16585	0.78	0.76	0.92	0.80	0.00	0.86	0.78	0.80	0.90
pericyte	9783	0.71	0.71	0.90	0.75	0.00	0.74	0.71	0.74	0.84
skeletal muscle satellite stem cell	5500	0.96	0.95	0.98	0.88	0.00	0.97	0.97	0.95	0.98
blood vessel smooth muscle cell	5405	0.86	0.82	0.96	0.74	0.00	0.96	0.88	0.87	0.96
regular atrial cardiac myocyte	5191	0.72	0.77	0.90	0.83	0.00	0.99	0.86	0.87	0.94
fibroblast of breast	4729	0.97	0.13	0.78	0.35	0.00	0.95	0.95	0.82	0.99
vascular associated smooth muscle cell	4547	0.71	0.40	0.80	0.60	0.00	0.78	0.66	0.71	0.80
myofibroblast cell	4013	0.63	0.76	0.91	0.61	0.00	0.76	0.60	0.67	0.85
thymic fibroblast type 2	3801	0.70	0.17	0.69	0.25	0.00	0.77	0.63	0.66	0.88
mesenchymal stem cell of adipose tissue	3414	0.35	0.05	0.77	0.54	0.00	0.49	0.39	0.43	0.55
stromal cell	3140	0.89	0.61	0.70	0.40	0.00	0.88	0.81	0.85	0.94
thymic fibroblast type 1	2935	0.67	0.30	0.79	0.28	0.00	0.84	0.57	0.55	0.86
ventricular cardiac muscle cell	2351	0.40	0.21	0.77	0.80	0.00	0.97	0.74	0.74	0.86
fibroblast of cardiac tissue	1751	0.69	0.94	0.98	0.48	0.00	0.93	0.75	0.74	0.96
alveolar adventitial fibroblast	988	0.81	0.80	0.73	0.37	0.00	0.84	0.62	0.85	0.95
adventitial cell	938	0.25	0.09	0.63	0.32	0.00	0.53	0.32	0.39	0.66
theca cell	918	0.70	0.61	0.92	0.82	0.00	0.50	0.79	0.69	0.89
keratocyte	887	0.49	0.34	0.56	0.19	0.00	0.61	0.47	0.44	0.72
myometrial cell	815	0.82	0.13	0.87	0.66	0.00	0.60	0.72	0.75	0.88
mural cell	554	0.46	0.69	0.84	0.39	0.00	0.78	0.55	0.58	0.92
Mueller cell	447	0.98	0.98	0.94	0.88	0.00	0.93	0.99	0.94	0.98
fast muscle cell	441	0.42	0.69	0.84	0.85	0.00	0.80	0.89	0.93	0.94
pancreatic stellate cell	396	0.61	0.05	0.84	0.40	0.00	0.64	0.70	0.77	0.80
tendon cell	380	0.50	0.58	0.77	0.52	0.00	0.42	0.42	0.39	0.79
muscle cell	372	0.72	0.13	0.79	0.89	0.00	0.92	0.98	1.00	0.99
Schwann cell	281	0.61	0.74	0.86	0.80	0.00	0.71	0.82	0.72	0.87
melanocyte	216	0.00	0.69	0.94	0.79	0.00	0.32	0.87	0.83	0.95
hepatic stellate cell	193	0.49	0.00	0.81	0.43	0.00	0.70	0.70	0.76	0.82
bronchial smooth muscle cell	204	0.38	0.44	0.65	0.35	0.00	0.49	0.53	0.56	0.73
tongue muscle cell	185	0.46	0.54	0.87	0.37	0.00	0.75	0.84	0.70	0.91
slow muscle cell	160	0.53	0.73	0.79	0.69	0.00	0.89	0.98	0.94	0.97
connective tissue cell	142	0.00	0.00	0.51	0.18	0.00	0.11	0.25	0.21	0.86
adipocyte	34	0.38	0.06	0.94	0.56	0.00	0.57	0.97	0.79	0.99
glial cell	19	0.00	0.00	0.75	0.48	0.00	0.05	0.31	0.15	0.36
Leydig cell	9	0.00	0.00	0.33	0.00	0.00	0.15	0.33	0.22	0.52
mesenchymal cell	2	0.00	0.00	0.00	0.00	0.00	0.02	0.31	0.57	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