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popV/
tabula_sapiens_Skin

Name: tabula_sapiens_Skin
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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
fibroblast	408	0.97	0.98	0.98	0.98	0.97	0.98	0.97	0.98
macrophage	324	0.97	0.97	0.97	0.96	0.95	0.97	0.96	0.98
T cell	267	0.68	0.76	0.76	0.74	0.72	0.71	0.83	0.82
endothelial cell	202	0.99	0.99	0.99	0.98	0.99	0.99	0.99	0.99
mast cell	213	0.99	0.99	0.98	0.99	0.99	0.99	0.99	0.99
CD8-positive, alpha-beta T cell	128	0.66	0.67	0.63	0.55	0.71	0.78	0.89	0.77
smooth muscle cell	60	0.87	0.90	0.90	0.91	0.86	0.87	0.85	0.87
CD4-positive, alpha-beta T cell	31	0.35	0.14	0.05	0.00	0.30	0.24	0.27	0.33
neutrophil	36	0.95	0.97	0.97	0.97	0.94	0.94	0.91	0.97
regulatory T cell	24	0.63	0.68	0.69	0.66	0.63	0.52	0.58	0.69
sebum secreting cell	13	0.86	0.86	0.86	0.89	0.89	0.89	0.77	0.86
myeloid dendritic cell	15	0.78	0.57	0.47	0.00	0.60	0.71	0.59	0.71
melanocyte	20	0.84	0.86	0.88	0.82	0.78	0.84	0.83	0.82
plasma cell	8	0.94	1.00	1.00	1.00	0.94	0.93	0.93	1.00
Langerhans cell	9	0.70	0.62	0.43	0.52	0.62	0.64	0.59	0.73
natural killer cell	4	0.60	0.00	0.00	0.40	0.20	0.36	0.40	0.50
mature NK T cell	4	0.00	0.00	0.00	0.00	0.40	0.00	0.40	0.00
keratocyte	3	0.36	0.00	0.00	0.80	0.67	1.00	0.80	0.80
basophil	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
epithelial cell	2	0.00	0.00	0.00	0.00	0.00	1.00	0.00	0.00
B cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
erythrocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
stromal cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
muscle cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
activated CD4-positive, alpha-beta T cell	0	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
fibroblast	3722	0.98	0.98	0.98	0.98	0.97	0.98	0.98	0.98
macrophage	2994	0.96	0.97	0.97	0.97	0.96	0.97	0.98	0.98
T cell	2369	0.68	0.78	0.78	0.77	0.75	0.81	0.89	0.85
endothelial cell	1873	0.99	0.99	0.99	0.99	0.99	1.00	0.99	0.99
mast cell	1788	0.99	0.99	0.99	0.99	0.98	0.99	0.99	0.99
CD8-positive, alpha-beta T cell	1403	0.69	0.75	0.73	0.66	0.76	0.89	0.94	0.84
smooth muscle cell	444	0.84	0.87	0.87	0.87	0.84	0.87	0.88	0.87
CD4-positive, alpha-beta T cell	334	0.26	0.20	0.22	0.04	0.45	0.59	0.70	0.61
neutrophil	254	0.97	0.99	0.98	0.98	0.95	0.97	0.98	0.99
regulatory T cell	249	0.62	0.68	0.71	0.68	0.79	0.82	0.85	0.80
sebum secreting cell	122	0.87	0.88	0.87	0.87	0.96	0.96	0.97	0.90
myeloid dendritic cell	93	0.54	0.49	0.48	0.23	0.61	0.72	0.81	0.75
melanocyte	86	0.81	0.81	0.81	0.81	0.87	0.98	0.96	0.89
plasma cell	78	0.98	0.98	0.99	0.94	0.90	0.96	0.99	0.98
Langerhans cell	67	0.56	0.55	0.66	0.56	0.67	0.73	0.78	0.81
natural killer cell	60	0.49	0.08	0.40	0.09	0.68	0.81	0.81	0.77
mature NK T cell	29	0.00	0.00	0.25	0.00	0.46	0.95	0.92	0.84
keratocyte	11	0.19	0.31	0.14	0.57	0.96	1.00	0.96	0.71
basophil	7	0.00	0.00	0.00	0.00	0.37	0.93	0.93	0.00
epithelial cell	6	0.00	0.00	0.00	0.00	0.63	1.00	1.00	0.29
B cell	7	0.00	0.22	0.25	0.44	0.48	0.93	0.88	1.00
erythrocyte	5	0.00	0.00	0.00	1.00	0.83	1.00	1.00	1.00
stromal cell	4	0.00	0.00	0.00	0.00	0.44	1.00	0.89	0.86
muscle cell	1	0.00	0.00	0.00	0.00	1.00	1.00	1.00	1.00
activated CD4-positive, alpha-beta T cell	1	0.00	0.00	0.00	0.00	0.18	1.00	1.00	1.00

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

popV/tabula_sapiens_Skin

Model description

Metrics

References

popV/
tabula_sapiens_Skin