popV/tabula_sapiens_Salivary_Gland

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
acinar cell of salivary gland	1234	0.96	0.94	0.97	0.96	0.00	0.94	0.96	0.97	0.97
B cell	510	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
fibroblast	465	0.97	0.94	0.97	0.95	0.00	0.92	0.96	0.95	0.98
CD8-positive, alpha-beta T cell	381	0.87	0.88	0.93	0.90	0.00	0.88	0.89	0.90	0.92
duct epithelial cell	377	0.87	0.78	0.92	0.86	0.00	0.83	0.87	0.88	0.90
CD4-positive, alpha-beta T cell	166	0.87	0.87	0.87	0.82	0.00	0.82	0.87	0.90	0.89
endothelial cell	160	0.93	0.90	0.92	0.89	0.00	0.93	0.95	0.95	0.97
macrophage	173	0.94	0.71	0.92	0.90	0.00	0.91	0.95	0.96	0.95
basal cell	108	0.87	0.90	0.91	0.87	0.00	0.87	0.85	0.87	0.89
tissue-resident macrophage	80	0.85	0.00	0.92	0.86	0.00	0.91	0.90	0.91	0.95
plasma cell	41	0.91	0.96	0.94	0.96	0.00	0.91	0.95	0.95	0.96
endothelial cell of lymphatic vessel	56	0.84	0.70	0.85	0.76	0.00	0.83	0.91	0.92	0.95
adventitial cell	56	0.84	0.30	0.75	0.72	0.00	0.65	0.77	0.72	0.80
vascular associated smooth muscle cell	44	0.98	0.98	0.98	0.92	0.00	0.93	0.97	0.98	0.97
neutrophil	25	0.91	0.88	0.91	1.00	0.00	0.98	0.92	0.94	0.93
myoepithelial cell	15	0.91	0.88	0.90	0.84	0.00	0.70	0.81	0.88	0.91
T cell	19	0.58	0.19	0.56	0.57	0.00	0.57	0.51	0.50	0.61
ionocyte	17	0.76	0.80	0.84	0.76	0.00	0.87	0.88	0.88	0.88
endothelial cell of artery	10	0.69	0.74	0.73	0.71	0.00	0.74	0.82	0.78	0.86
monocyte	10	0.47	0.57	0.69	0.52	0.00	0.45	0.53	0.64	0.57
natural killer cell	9	0.45	0.43	0.62	0.00	0.00	0.50	0.53	0.41	0.58
mast cell	5	0.00	0.77	0.67	0.50	0.00	0.77	0.60	0.80	0.80
classical monocyte	9	0.00	0.00	0.00	0.20	0.00	0.33	0.36	0.14	0.00
intermediate monocyte	7	0.00	0.00	0.50	0.20	0.00	0.00	0.00	0.40	0.00
mature NK T cell	3	0.00	0.00	0.00	0.00	0.00	0.40	0.33	0.40	0.00
leukocyte	1	0.00	0.00	0.00	0.00	0.00	0.33	1.00	0.00	0.00
pericyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
salivary gland cell	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
myeloid dendritic cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
hematopoietic precursor cell	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
non-classical monocyte	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
acinar cell of salivary gland	11003	0.96	0.94	0.97	0.96	0.00	0.95	0.96	0.96	0.98
B cell	4438	0.99	0.99	0.99	0.98	0.00	0.99	0.99	0.99	0.99
fibroblast	4002	0.97	0.95	0.98	0.96	0.00	0.95	0.97	0.96	0.99
CD8-positive, alpha-beta T cell	3684	0.86	0.87	0.93	0.91	0.00	0.89	0.90	0.91	0.93
duct epithelial cell	3512	0.87	0.78	0.93	0.88	0.00	0.87	0.88	0.89	0.92
CD4-positive, alpha-beta T cell	1720	0.88	0.88	0.90	0.86	0.00	0.86	0.90	0.90	0.91
endothelial cell	1469	0.93	0.90	0.93	0.94	0.00	0.96	0.97	0.97	0.98
macrophage	1450	0.93	0.72	0.95	0.92	0.00	0.94	0.97	0.97	0.98
basal cell	1074	0.90	0.93	0.95	0.90	0.00	0.91	0.94	0.95	0.95
tissue-resident macrophage	574	0.73	0.01	0.91	0.91	0.00	0.90	0.85	0.88	0.90
plasma cell	542	0.93	0.97	0.97	0.95	0.00	0.95	0.99	0.99	0.98
endothelial cell of lymphatic vessel	490	0.88	0.68	0.86	0.88	0.00	0.91	0.95	0.96	0.97
adventitial cell	404	0.83	0.34	0.83	0.74	0.00	0.76	0.80	0.80	0.92
vascular associated smooth muscle cell	359	0.95	0.96	0.94	0.93	0.00	0.96	0.97	0.97	0.97
neutrophil	218	0.94	0.88	0.93	0.95	0.00	0.97	0.96	0.97	0.96
myoepithelial cell	201	0.93	0.94	0.90	0.90	0.00	0.78	0.91	0.91	0.95
T cell	174	0.66	0.29	0.74	0.70	0.00	0.73	0.81	0.83	0.85
ionocyte	125	0.84	0.91	0.91	0.80	0.00	0.74	0.93	0.91	0.94
endothelial cell of artery	106	0.74	0.75	0.82	0.79	0.00	0.80	0.91	0.92	0.92
monocyte	89	0.49	0.60	0.61	0.56	0.00	0.62	0.91	0.89	0.80
natural killer cell	64	0.39	0.58	0.46	0.30	0.00	0.42	0.60	0.56	0.70
mast cell	40	0.00	0.76	0.70	0.59	0.00	0.80	1.00	1.00	0.97
classical monocyte	34	0.00	0.00	0.05	0.23	0.00	0.87	0.97	0.93	0.67
intermediate monocyte	35	0.00	0.00	0.51	0.37	0.00	0.72	0.80	0.91	0.90
mature NK T cell	20	0.00	0.00	0.00	0.00	0.00	0.47	0.74	0.75	0.67
leukocyte	5	0.00	0.00	0.33	0.00	0.00	0.29	0.91	0.91	1.00
pericyte	3	0.00	0.00	0.00	0.00	0.00	1.00	1.00	1.00	0.00
salivary gland cell	1	0.00	0.00	0.00	0.00	0.00	0.03	1.00	1.00	1.00
myeloid dendritic cell	1	0.00	0.00	0.00	0.00	0.00	0.29	1.00	1.00	0.00
hematopoietic precursor cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
non-classical monocyte	1	0.00	0.00	0.00	0.00	0.00	0.00	1.00	1.00	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