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 bbknn	knn harmony	knn on scvi	onclass	scanvi	svm	xgboost	Consensus Prediction
fibroblast	8243	0.81	0.79	0.88	0.72	0.00	0.65	0.67	0.74	0.88
stromal cell of ovary	3498	0.98	0.95	0.90	0.72	0.00	0.38	0.97	0.97	0.99
mesenchymal stem cell	2271	0.93	0.77	0.89	0.41	0.00	0.06	0.89	0.90	0.95
smooth muscle cell	1811	0.79	0.66	0.84	0.72	0.00	0.65	0.75	0.82	0.84
pericyte	1112	0.74	0.65	0.83	0.68	0.00	0.55	0.68	0.75	0.79
skeletal muscle satellite stem cell	670	0.94	0.95	0.96	0.81	0.00	0.73	0.95	0.95	0.97
blood vessel smooth muscle cell	584	0.81	0.41	0.93	0.65	0.00	0.36	0.87	0.86	0.93
regular atrial cardiac myocyte	619	0.82	0.47	0.74	0.52	0.00	0.14	0.89	0.95	0.93
fibroblast of breast	548	0.96	0.00	0.68	0.11	0.00	0.00	0.89	0.85	0.88
vascular associated smooth muscle cell	473	0.76	0.05	0.64	0.49	0.00	0.26	0.60	0.72	0.74
myofibroblast cell	418	0.68	0.43	0.81	0.46	0.00	0.31	0.56	0.63	0.77
thymic fibroblast type 2	406	0.65	0.00	0.39	0.15	0.00	0.03	0.58	0.61	0.39
mesenchymal stem cell of adipose tissue	365	0.35	0.00	0.64	0.36	0.00	0.33	0.37	0.38	0.52
stromal cell	285	0.86	0.01	0.61	0.29	0.00	0.37	0.85	0.83	0.94
thymic fibroblast type 1	336	0.58	0.02	0.57	0.17	0.00	0.07	0.55	0.60	0.56
ventricular cardiac muscle cell	244	0.43	0.00	0.62	0.47	0.00	0.48	0.77	0.88	0.84
fibroblast of cardiac tissue	187	0.96	0.64	0.92	0.11	0.00	0.34	0.72	0.78	0.95
alveolar adventitial fibroblast	124	0.74	0.33	0.65	0.10	0.00	0.13	0.62	0.81	0.75
adventitial cell	110	0.22	0.04	0.17	0.04	0.00	0.16	0.31	0.35	0.38
theca cell	121	0.78	0.31	0.88	0.62	0.00	0.63	0.81	0.73	0.87
keratocyte	91	0.56	0.04	0.29	0.02	0.00	0.17	0.46	0.46	0.43
myometrial cell	102	0.66	0.00	0.86	0.55	0.00	0.55	0.63	0.78	0.85
mural cell	64	0.71	0.55	0.68	0.15	0.00	0.31	0.55	0.66	0.84
Mueller cell	50	0.98	0.80	0.95	0.82	0.00	0.81	0.95	0.92	0.98
fast muscle cell	53	0.53	0.74	0.83	0.71	0.00	0.81	0.83	0.88	0.92
pancreatic stellate cell	37	0.61	0.00	0.53	0.25	0.00	0.11	0.65	0.79	0.82
tendon cell	40	0.63	0.14	0.41	0.00	0.00	0.10	0.37	0.36	0.59
muscle cell	32	0.72	0.00	0.77	0.75	0.00	0.44	0.94	0.94	0.97
Schwann cell	27	0.75	0.81	0.92	0.89	0.00	0.30	0.71	0.60	0.86
melanocyte	16	0.00	0.63	0.80	0.69	0.00	0.29	0.43	0.77	0.79
hepatic stellate cell	27	0.50	0.00	0.41	0.30	0.00	0.24	0.72	0.82	0.84
bronchial smooth muscle cell	13	0.26	0.14	0.00	0.14	0.00	0.27	0.28	0.25	0.50
tongue muscle cell	11	0.43	0.31	0.62	0.00	0.00	0.09	0.37	0.40	0.62
slow muscle cell	15	0.56	0.37	0.68	0.21	0.00	0.36	0.85	0.97	0.93
connective tissue cell	8	0.00	0.00	0.00	0.00	0.00	0.02	0.11	0.18	0.00
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	0.00	0.00	0.03	0.17	0.09	0.25
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 bbknn	knn harmony	knn on scvi	onclass	scanvi	svm	xgboost	Consensus Prediction
fibroblast	74894	0.81	0.79	0.90	0.73	0.00	0.88	0.67	0.75	0.91
stromal cell of ovary	31505	0.98	0.94	0.87	0.70	0.00	0.96	0.97	0.97	0.99
mesenchymal stem cell	21225	0.94	0.77	0.91	0.46	0.00	0.96	0.89	0.90	0.97
smooth muscle cell	16578	0.79	0.66	0.88	0.76	0.00	0.82	0.76	0.80	0.88
pericyte	9765	0.73	0.65	0.86	0.73	0.00	0.75	0.71	0.76	0.82
skeletal muscle satellite stem cell	5498	0.95	0.94	0.97	0.87	0.00	0.94	0.95	0.96	0.97
blood vessel smooth muscle cell	5403	0.81	0.43	0.95	0.76	0.00	0.93	0.87	0.88	0.95
regular atrial cardiac myocyte	5192	0.80	0.48	0.87	0.84	0.00	0.99	0.90	0.94	0.94
fibroblast of breast	4722	0.96	0.00	0.65	0.22	0.00	0.99	0.88	0.85	0.99
vascular associated smooth muscle cell	4545	0.76	0.06	0.74	0.55	0.00	0.75	0.64	0.73	0.81
myofibroblast cell	4017	0.67	0.42	0.87	0.60	0.00	0.63	0.61	0.67	0.82
thymic fibroblast type 2	3797	0.66	0.00	0.55	0.18	0.00	0.91	0.59	0.62	0.86
mesenchymal stem cell of adipose tissue	3407	0.35	0.00	0.69	0.46	0.00	0.53	0.38	0.41	0.53
stromal cell	3143	0.86	0.01	0.62	0.37	0.00	0.87	0.83	0.85	0.94
thymic fibroblast type 1	2933	0.57	0.01	0.70	0.18	0.00	0.86	0.54	0.58	0.84
ventricular cardiac muscle cell	2354	0.40	0.00	0.72	0.68	0.00	0.96	0.81	0.89	0.85
fibroblast of cardiac tissue	1750	0.96	0.55	0.97	0.25	0.00	0.96	0.73	0.78	0.97
alveolar adventitial fibroblast	987	0.75	0.41	0.58	0.12	0.00	0.80	0.59	0.82	0.93
adventitial cell	934	0.21	0.00	0.37	0.06	0.00	0.52	0.31	0.37	0.57
theca cell	917	0.76	0.26	0.91	0.72	0.00	0.55	0.75	0.69	0.88
keratocyte	883	0.55	0.04	0.38	0.03	0.00	0.55	0.46	0.50	0.68
myometrial cell	815	0.60	0.00	0.85	0.69	0.00	0.71	0.63	0.73	0.84
mural cell	550	0.68	0.52	0.75	0.22	0.00	0.67	0.54	0.64	0.92
Mueller cell	445	0.98	0.82	0.93	0.88	0.00	0.94	0.95	0.93	0.98
fast muscle cell	442	0.53	0.68	0.85	0.78	0.00	0.87	0.86	0.92	0.94
pancreatic stellate cell	387	0.56	0.00	0.77	0.33	0.00	0.64	0.64	0.76	0.78
tendon cell	380	0.67	0.16	0.72	0.24	0.00	0.43	0.41	0.41	0.82
muscle cell	374	0.80	0.00	0.84	0.89	0.00	0.84	0.97	0.99	0.99
Schwann cell	285	0.61	0.68	0.84	0.73	0.00	0.52	0.74	0.80	0.87
melanocyte	216	0.00	0.69	0.89	0.64	0.00	0.45	0.61	0.78	0.94
hepatic stellate cell	195	0.45	0.00	0.65	0.47	0.00	0.64	0.62	0.73	0.82
bronchial smooth muscle cell	206	0.40	0.05	0.40	0.13	0.00	0.46	0.45	0.56	0.68
tongue muscle cell	187	0.45	0.24	0.75	0.11	0.00	0.47	0.58	0.62	0.86
slow muscle cell	159	0.57	0.42	0.80	0.47	0.00	0.75	0.89	0.95	0.97
connective tissue cell	143	0.00	0.00	0.07	0.08	0.00	0.42	0.22	0.30	0.54
adipocyte	33	0.64	0.00	0.92	0.36	0.00	0.25	0.77	0.90	0.99
glial cell	19	0.00	0.00	0.70	0.33	0.00	0.10	0.34	0.18	0.55
Leydig cell	9	0.00	0.00	0.00	0.00	0.00	0.15	0.44	0.27	0.74
mesenchymal cell	2	0.00	0.00	0.00	0.00	0.00	0.07	0.10	0.57	0.67

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