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	8324	0.80	0.87	0.87	0.66	0.00	0.75	0.69	0.77	0.89
stromal cell of ovary	3503	0.97	0.96	0.86	0.57	0.00	0.77	0.96	0.97	0.98
mesenchymal stem cell	2264	0.93	0.91	0.87	0.33	0.00	0.53	0.88	0.90	0.96
smooth muscle cell	1815	0.78	0.77	0.85	0.67	0.00	0.68	0.75	0.81	0.85
pericyte	1122	0.73	0.75	0.81	0.62	0.00	0.58	0.64	0.73	0.80
skeletal muscle satellite stem cell	667	0.96	0.96	0.96	0.73	0.00	0.78	0.93	0.96	0.97
blood vessel smooth muscle cell	575	0.78	0.79	0.91	0.66	0.00	0.71	0.85	0.87	0.92
regular atrial cardiac myocyte	619	0.85	0.82	0.65	0.31	0.00	0.66	0.94	0.97	0.96
fibroblast of breast	541	0.98	0.31	0.62	0.04	0.00	0.00	0.90	0.86	0.88
vascular associated smooth muscle cell	472	0.73	0.36	0.58	0.20	0.00	0.30	0.63	0.71	0.74
myofibroblast cell	416	0.56	0.76	0.79	0.30	0.00	0.54	0.57	0.59	0.78
thymic fibroblast type 2	404	0.65	0.14	0.42	0.07	0.00	0.16	0.64	0.67	0.52
mesenchymal stem cell of adipose tissue	364	0.35	0.08	0.64	0.24	0.00	0.31	0.35	0.40	0.52
stromal cell	297	0.83	0.58	0.57	0.08	0.00	0.46	0.73	0.81	0.91
thymic fibroblast type 1	334	0.60	0.39	0.59	0.08	0.00	0.05	0.59	0.62	0.66
ventricular cardiac muscle cell	244	0.49	0.22	0.54	0.46	0.00	0.66	0.86	0.92	0.90
fibroblast of cardiac tissue	194	0.96	0.94	0.89	0.01	0.00	0.40	0.69	0.83	0.98
alveolar adventitial fibroblast	122	0.84	0.81	0.61	0.10	0.00	0.03	0.63	0.78	0.84
adventitial cell	107	0.26	0.07	0.27	0.05	0.00	0.14	0.34	0.40	0.41
theca cell	119	0.77	0.80	0.90	0.61	0.00	0.76	0.71	0.72	0.88
keratocyte	90	0.53	0.58	0.58	0.02	0.00	0.14	0.40	0.51	0.66
myometrial cell	102	0.75	0.41	0.85	0.18	0.00	0.51	0.58	0.71	0.86
mural cell	58	0.66	0.81	0.73	0.19	0.00	0.33	0.48	0.53	0.88
Mueller cell	50	0.99	1.00	0.95	0.74	0.00	0.72	0.98	0.94	0.97
fast muscle cell	53	0.73	0.73	0.86	0.75	0.00	0.79	0.73	0.89	0.89
pancreatic stellate cell	38	0.64	0.00	0.46	0.11	0.00	0.00	0.56	0.72	0.74
tendon cell	40	0.30	0.65	0.53	0.08	0.00	0.35	0.28	0.37	0.73
muscle cell	35	0.73	0.11	0.79	0.79	0.00	0.80	0.89	0.96	0.97
Schwann cell	35	0.85	0.81	0.87	0.76	0.00	0.63	0.61	0.68	0.86
melanocyte	16	0.76	0.67	0.87	0.38	0.00	0.36	0.59	0.71	0.89
hepatic stellate cell	29	0.78	0.00	0.73	0.33	0.00	0.13	0.62	0.83	0.85
bronchial smooth muscle cell	12	0.24	0.40	0.16	0.00	0.00	0.11	0.15	0.26	0.32
tongue muscle cell	15	0.57	0.70	0.64	0.00	0.00	0.18	0.40	0.46	0.70
slow muscle cell	14	0.72	0.70	0.73	0.50	0.00	0.59	0.76	0.96	0.93
connective tissue cell	10	0.00	0.00	0.17	0.09	0.00	0.12	0.16	0.22	0.44
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	1.00	1.00	0.00	0.17	0.20	0.00	0.50
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	74863	0.80	0.85	0.91	0.75	0.00	0.88	0.69	0.77	0.92
stromal cell of ovary	31500	0.97	0.95	0.86	0.68	0.00	0.97	0.96	0.97	0.99
mesenchymal stem cell	21232	0.93	0.90	0.91	0.49	0.00	0.96	0.88	0.90	0.97
smooth muscle cell	16590	0.78	0.74	0.90	0.76	0.00	0.86	0.75	0.81	0.89
pericyte	9756	0.71	0.71	0.89	0.73	0.00	0.76	0.67	0.75	0.83
skeletal muscle satellite stem cell	5501	0.96	0.96	0.98	0.82	0.00	0.94	0.93	0.95	0.97
blood vessel smooth muscle cell	5412	0.79	0.77	0.95	0.75	0.00	0.94	0.86	0.88	0.94
regular atrial cardiac myocyte	5193	0.82	0.75	0.87	0.74	0.00	0.99	0.94	0.97	0.97
fibroblast of breast	4729	0.98	0.22	0.68	0.26	0.00	0.97	0.89	0.86	0.99
vascular associated smooth muscle cell	4546	0.73	0.27	0.73	0.48	0.00	0.78	0.67	0.73	0.82
myofibroblast cell	4019	0.57	0.74	0.88	0.56	0.00	0.74	0.58	0.62	0.83
thymic fibroblast type 2	3801	0.66	0.12	0.61	0.24	0.00	0.85	0.67	0.67	0.89
mesenchymal stem cell of adipose tissue	3411	0.36	0.04	0.73	0.46	0.00	0.51	0.35	0.43	0.55
stromal cell	3141	0.84	0.51	0.66	0.32	0.00	0.91	0.78	0.84	0.94
thymic fibroblast type 1	2935	0.58	0.27	0.75	0.25	0.00	0.82	0.64	0.63	0.86
ventricular cardiac muscle cell	2354	0.44	0.22	0.76	0.74	0.00	0.97	0.88	0.94	0.93
fibroblast of cardiac tissue	1750	0.95	0.93	0.97	0.35	0.00	0.76	0.68	0.79	0.98
alveolar adventitial fibroblast	989	0.83	0.79	0.64	0.24	0.00	0.91	0.65	0.80	0.92
adventitial cell	937	0.27	0.03	0.51	0.25	0.00	0.67	0.34	0.41	0.65
theca cell	919	0.74	0.74	0.90	0.79	0.00	0.64	0.67	0.71	0.88
keratocyte	889	0.56	0.47	0.60	0.12	0.00	0.59	0.42	0.51	0.68
myometrial cell	815	0.70	0.16	0.87	0.46	0.00	0.75	0.60	0.70	0.86
mural cell	557	0.63	0.74	0.82	0.34	0.00	0.86	0.50	0.57	0.94
Mueller cell	447	0.99	0.96	0.94	0.86	0.00	0.81	0.99	0.95	0.98
fast muscle cell	442	0.75	0.67	0.88	0.84	0.00	0.86	0.77	0.93	0.93
pancreatic stellate cell	394	0.59	0.01	0.79	0.26	0.00	0.67	0.54	0.75	0.79
tendon cell	380	0.31	0.64	0.80	0.36	0.00	0.51	0.33	0.40	0.74
muscle cell	371	0.80	0.13	0.87	0.89	0.00	0.91	0.90	0.99	0.99
Schwann cell	280	0.73	0.74	0.87	0.69	0.00	0.66	0.60	0.71	0.87
melanocyte	216	0.78	0.72	0.94	0.63	0.00	0.55	0.69	0.81	0.96
hepatic stellate cell	193	0.66	0.00	0.85	0.41	0.00	0.74	0.57	0.77	0.85
bronchial smooth muscle cell	207	0.43	0.40	0.60	0.27	0.00	0.46	0.40	0.59	0.71
tongue muscle cell	187	0.49	0.60	0.81	0.18	0.00	0.82	0.47	0.61	0.90
slow muscle cell	160	0.77	0.76	0.82	0.69	0.00	0.75	0.80	0.92	0.96
connective tissue cell	142	0.00	0.00	0.40	0.35	0.00	0.50	0.28	0.32	0.82
adipocyte	34	0.00	0.13	0.96	0.77	0.00	0.42	0.99	0.80	0.96
glial cell	19	0.00	0.00	0.71	0.52	0.00	0.26	0.34	0.18	0.75
Leydig cell	9	0.00	0.00	0.00	0.17	0.00	0.16	0.67	0.33	0.67
mesenchymal cell	2	0.00	0.00	0.00	0.00	0.00	0.01	0.67	0.80	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