You can deploy this model and start earning money today!

popV/
tabula_sapiens_Bladder

Views

No views yet

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	scanvi	svm	xgboost	Consensus Prediction
bladder urothelial cell	2776	0.99	0.99	0.99	0.99	0.95	0.99	0.99	0.99
fibroblast	1377	0.95	0.97	0.98	0.97	0.94	0.96	0.96	0.97
monocyte	457	0.88	0.90	0.92	0.93	0.90	0.89	0.89	0.93
CD8-positive, alpha-beta T cell	413	0.85	0.88	0.90	0.80	0.87	0.86	0.90	0.91
macrophage	336	0.86	0.89	0.92	0.92	0.91	0.88	0.89	0.92
myofibroblast cell	317	0.85	0.91	0.93	0.92	0.82	0.89	0.88	0.91
CD4-positive, alpha-beta T cell	224	0.69	0.76	0.78	0.59	0.73	0.73	0.83	0.84
mast cell	165	0.97	0.99	0.98	0.99	0.97	0.99	0.98	0.99
plasma cell	132	0.95	0.93	0.97	0.98	0.95	0.97	0.95	0.97
pericyte	112	0.93	0.96	0.95	0.95	0.92	0.96	0.95	0.96
smooth muscle cell	97	0.96	0.97	0.97	0.98	0.89	0.96	0.93	0.96
T cell	64	0.43	0.08	0.40	0.21	0.47	0.43	0.54	0.58
B cell	51	0.98	0.98	0.98	0.97	0.94	0.94	0.93	0.98
vein endothelial cell	37	0.82	0.88	0.89	0.84	0.80	0.87	0.89	0.90
neutrophil	24	0.96	0.98	1.00	0.94	0.67	0.94	0.91	0.96
natural killer cell	13	0.63	0.19	0.71	0.38	0.20	0.56	0.67	0.74
endothelial cell of lymphatic vessel	14	0.90	0.90	0.90	0.76	0.65	0.93	0.90	0.90
capillary endothelial cell	7	0.40	0.36	0.67	0.55	0.60	0.86	0.92	0.83
erythrocyte	12	0.91	0.32	0.88	0.91	0.31	0.89	0.75	0.96
mature NK T cell	7	0.62	0.44	0.46	0.60	0.60	0.78	0.71	0.71
endothelial cell	2	0.00	0.00	0.00	0.00	0.25	0.00	0.00	0.00
regulatory T cell	2	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	scanvi	svm	xgboost	Consensus Prediction
bladder urothelial cell	24465	0.99	0.99	0.99	0.99	0.96	0.99	0.99	0.99
fibroblast	12389	0.95	0.97	0.98	0.97	0.93	0.96	0.95	0.97
monocyte	4398	0.89	0.92	0.94	0.94	0.91	0.91	0.91	0.94
CD8-positive, alpha-beta T cell	4019	0.85	0.89	0.90	0.82	0.88	0.88	0.91	0.92
macrophage	2816	0.84	0.88	0.91	0.91	0.89	0.88	0.88	0.92
myofibroblast cell	2819	0.85	0.91	0.92	0.91	0.80	0.89	0.87	0.91
CD4-positive, alpha-beta T cell	1965	0.67	0.74	0.77	0.61	0.76	0.81	0.87	0.84
mast cell	1403	0.97	0.98	0.98	0.98	0.97	0.99	0.98	0.99
plasma cell	1073	0.96	0.97	0.98	0.98	0.97	0.98	0.97	0.98
pericyte	1072	0.96	0.96	0.96	0.96	0.92	0.97	0.96	0.97
smooth muscle cell	956	0.95	0.96	0.97	0.97	0.88	0.96	0.95	0.96
T cell	717	0.42	0.17	0.51	0.29	0.55	0.61	0.68	0.71
B cell	433	0.95	0.94	0.94	0.95	0.92	0.95	0.95	0.96
vein endothelial cell	401	0.82	0.87	0.88	0.86	0.94	0.96	0.97	0.91
neutrophil	217	0.95	0.96	0.97	0.93	0.69	0.95	0.91	0.95
natural killer cell	152	0.58	0.39	0.63	0.39	0.28	0.76	0.77	0.79
endothelial cell of lymphatic vessel	113	0.89	0.90	0.90	0.84	0.78	0.98	0.97	0.94
capillary endothelial cell	100	0.36	0.58	0.61	0.52	0.83	0.98	0.99	0.78
erythrocyte	94	0.93	0.39	0.96	0.89	0.37	0.90	0.79	0.98
mature NK T cell	88	0.53	0.47	0.67	0.23	0.75	0.82	0.88	0.89
endothelial cell	35	0.00	0.00	0.05	0.29	0.72	0.96	0.96	0.65
regulatory T cell	21	0.00	0.00	0.00	0.00	0.32	0.75	0.72	0.65

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

popV/tabula_sapiens_Bladder

Model description

Metrics

References

popV/
tabula_sapiens_Bladder