popV/tabula_sapiens_Tongue

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
basal cell	1643	0.86	0.89	0.93	0.91	0.00	0.85	0.86	0.89	0.91
stratified squamous epithelial cell	1174	0.85	0.88	0.91	0.89	0.00	0.84	0.83	0.86	0.88
CD4-positive, alpha-beta T cell	156	0.69	0.71	0.76	0.68	0.00	0.68	0.71	0.73	0.77
fibroblast	179	0.98	0.96	0.98	0.97	0.00	0.96	0.97	0.96	0.97
B cell	125	0.98	0.98	0.98	0.94	0.00	0.95	0.96	0.96	0.98
endothelial cell	131	0.96	0.98	0.99	0.98	0.00	0.99	0.98	0.97	0.98
CD8-positive, alpha-beta T cell	124	0.75	0.75	0.78	0.69	0.00	0.77	0.75	0.77	0.78
salivary gland cell	83	0.89	0.18	0.92	0.86	0.00	0.72	0.89	0.87	0.93
mural cell	60	0.92	0.91	0.94	0.92	0.00	0.91	0.93	0.94	0.93
macrophage	55	0.79	0.82	0.85	0.84	0.00	0.80	0.80	0.78	0.83
myoepithelial cell	27	0.84	0.00	0.93	0.92	0.00	0.73	0.87	0.86	0.90
tongue muscle cell	13	0.81	0.85	0.85	0.83	0.00	0.73	0.81	0.76	0.81
T cell	20	0.33	0.00	0.33	0.27	0.00	0.35	0.18	0.36	0.33
neutrophil	18	0.97	1.00	1.00	0.95	0.00	0.95	1.00	0.97	0.97
monocyte	12	0.58	0.56	0.62	0.54	0.00	0.47	0.47	0.32	0.64
plasma cell	9	0.94	0.88	1.00	0.57	0.00	0.70	1.00	0.94	1.00
endothelial cell of lymphatic vessel	7	0.71	0.71	0.71	0.86	0.00	0.63	0.92	0.73	0.77
regulatory T cell	9	0.32	0.20	0.57	0.00	0.00	0.50	0.50	0.76	0.46
mast cell	11	0.88	0.83	0.83	0.85	0.00	0.85	0.88	0.88	0.88
Schwann cell	4	0.62	0.50	0.55	0.57	0.00	0.50	0.67	0.67	0.62
taste receptor cell	2	0.67	0.67	0.67	0.67	0.00	0.25	0.67	0.50	0.67
myeloid dendritic cell	4	0.00	0.00	0.00	0.00	0.00	0.33	0.40	0.00	0.00
natural killer 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
basal cell	14620	0.87	0.90	0.95	0.93	0.00	0.87	0.88	0.90	0.92
stratified squamous epithelial cell	11139	0.86	0.91	0.94	0.92	0.00	0.87	0.87	0.89	0.91
CD4-positive, alpha-beta T cell	1431	0.73	0.76	0.82	0.75	0.00	0.81	0.83	0.85	0.86
fibroblast	1352	0.98	0.97	0.98	0.97	0.00	0.97	0.97	0.98	0.98
B cell	1125	0.99	0.98	0.98	0.95	0.00	0.98	0.99	0.99	0.99
endothelial cell	1090	0.95	0.98	0.98	0.97	0.00	0.98	0.98	0.98	0.98
CD8-positive, alpha-beta T cell	983	0.76	0.77	0.81	0.70	0.00	0.82	0.84	0.87	0.84
salivary gland cell	765	0.87	0.17	0.92	0.87	0.00	0.72	0.93	0.92	0.92
mural cell	558	0.91	0.91	0.94	0.93	0.00	0.94	0.97	0.96	0.94
macrophage	515	0.80	0.88	0.88	0.86	0.00	0.90	0.96	0.95	0.92
myoepithelial cell	243	0.84	0.03	0.90	0.86	0.00	0.77	0.91	0.90	0.92
tongue muscle cell	189	0.85	0.85	0.88	0.84	0.00	0.83	0.97	0.95	0.92
T cell	174	0.46	0.00	0.41	0.31	0.00	0.64	0.76	0.82	0.75
neutrophil	136	0.92	0.95	0.96	0.95	0.00	0.96	0.98	0.97	0.97
monocyte	127	0.62	0.67	0.67	0.65	0.00	0.68	0.94	0.96	0.86
plasma cell	106	0.94	0.93	0.98	0.73	0.00	0.80	0.99	1.00	1.00
endothelial cell of lymphatic vessel	90	0.94	0.95	0.95	0.86	0.00	0.83	0.97	0.98	0.96
regulatory T cell	83	0.54	0.30	0.65	0.00	0.00	0.78	0.86	0.88	0.84
mast cell	65	0.96	0.98	0.98	0.94	0.00	0.94	0.98	0.97	0.98
Schwann cell	31	0.57	0.66	0.72	0.69	0.00	0.85	0.93	0.94	0.85
taste receptor cell	30	0.82	0.60	0.78	0.78	0.00	0.38	0.97	0.74	0.89
myeloid dendritic cell	18	0.00	0.00	0.00	0.00	0.00	0.77	1.00	1.00	0.62
natural killer cell	8	0.00	0.00	0.00	0.00	0.00	0.56	0.94	0.94	0.55

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