popV/tabula_sapiens_Stomach

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	646	0.97	0.96	0.98	0.96	0.00	0.95	0.96	0.97	0.99
CD4-positive, alpha-beta T cell	568	0.90	0.91	0.89	0.84	0.00	0.83	0.90	0.91	0.91
mononuclear phagocyte	514	0.96	0.90	0.97	0.89	0.00	0.92	0.94	0.94	0.97
plasma cell	418	0.99	0.98	0.95	0.89	0.00	0.94	1.00	1.00	0.99
B cell	213	0.96	0.94	0.94	0.84	0.00	0.92	0.94	0.92	0.96
epithelial cell	170	0.97	0.97	0.98	0.93	0.00	0.96	0.98	0.99	0.99
CD8-positive, alpha-beta T cell	168	0.65	0.72	0.72	0.65	0.00	0.61	0.71	0.74	0.72
macrophage	108	0.77	0.20	0.82	0.38	0.00	0.70	0.76	0.77	0.82
monocyte	116	0.88	0.89	0.91	0.89	0.00	0.84	0.83	0.83	0.91
mast cell	106	0.99	0.99	1.00	0.94	0.00	0.93	1.00	0.99	1.00
neutrophil	98	1.00	1.00	0.99	0.97	0.00	0.98	0.99	0.99	1.00
tissue-resident macrophage	58	0.75	0.07	0.81	0.82	0.00	0.76	0.72	0.79	0.92
endothelial cell of lymphatic vessel	52	0.99	0.96	0.98	0.97	0.00	0.91	0.97	0.96	0.98
regulatory T cell	22	0.53	0.00	0.17	0.00	0.00	0.44	0.60	0.89	0.56
natural killer cell	11	0.49	0.48	0.48	0.54	0.00	0.39	0.50	0.48	0.52
mature NK T cell	11	0.22	0.17	0.40	0.38	0.00	0.37	0.67	0.58	0.55
T cell	10	0.00	0.00	0.00	0.00	0.00	0.08	0.35	0.11	0.00
interstitial cell of Cajal	4	0.89	0.00	1.00	0.89	0.00	0.50	1.00	1.00	1.00
smooth muscle cell	3	0.55	0.50	0.50	0.40	0.00	0.55	0.44	0.60	0.60
enteroendocrine cell	1	1.00	1.00	1.00	0.00	0.00	0.22	1.00	1.00	1.00

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	5899	0.97	0.95	0.98	0.96	0.00	0.97	0.97	0.97	0.99
CD4-positive, alpha-beta T cell	5216	0.91	0.93	0.93	0.86	0.00	0.88	0.92	0.94	0.94
mononuclear phagocyte	4822	0.96	0.90	0.97	0.92	0.00	0.95	0.95	0.95	0.97
plasma cell	3759	0.99	0.97	0.96	0.90	0.00	0.96	0.99	0.99	0.99
B cell	1968	0.94	0.93	0.95	0.86	0.00	0.93	0.95	0.93	0.95
epithelial cell	1428	0.97	0.97	0.98	0.93	0.00	0.96	0.98	0.98	0.98
CD8-positive, alpha-beta T cell	1418	0.72	0.77	0.79	0.68	0.00	0.75	0.81	0.82	0.82
macrophage	955	0.79	0.25	0.83	0.63	0.00	0.81	0.84	0.86	0.87
monocyte	938	0.85	0.86	0.88	0.87	0.00	0.85	0.85	0.86	0.89
mast cell	861	0.98	0.97	0.97	0.94	0.00	0.93	0.98	0.98	0.98
neutrophil	830	1.00	0.99	0.99	0.97	0.00	0.99	0.99	0.99	1.00
tissue-resident macrophage	589	0.75	0.10	0.84	0.79	0.00	0.81	0.75	0.82	0.90
endothelial cell of lymphatic vessel	498	0.99	0.99	0.98	0.93	0.00	0.96	0.99	0.98	0.99
regulatory T cell	207	0.41	0.03	0.33	0.02	0.00	0.49	0.66	0.92	0.62
natural killer cell	112	0.66	0.74	0.77	0.69	0.00	0.72	0.90	0.88	0.86
mature NK T cell	76	0.48	0.10	0.49	0.43	0.00	0.62	0.86	0.83	0.87
T cell	66	0.00	0.00	0.03	0.09	0.00	0.40	0.77	0.75	0.78
interstitial cell of Cajal	67	0.80	0.00	0.86	0.86	0.00	0.63	0.96	0.90	0.91
smooth muscle cell	24	0.61	0.65	0.56	0.54	0.00	0.52	0.80	0.84	0.81
enteroendocrine cell	24	0.86	0.33	0.85	0.64	0.00	0.61	0.94	0.89	0.92

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