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popV/
tabula_sapiens_Kidney

Name: tabula_sapiens_Kidney
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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
kidney epithelial cell	929	0.99	0.99	1.00	1.00	0.98	1.00	1.00	1.00
CD8-positive, alpha-beta T cell	45	0.83	0.86	0.91	0.86	0.84	0.90	0.89	0.92
B cell	48	0.97	0.88	0.98	0.96	0.94	0.95	0.98	0.97
macrophage	40	0.83	0.74	0.88	0.82	0.66	0.79	0.84	0.88
CD4-positive, alpha-beta T cell	29	0.81	0.91	0.94	0.83	0.84	0.85	0.93	0.90
natural killer cell	18	0.92	0.92	0.92	0.97	0.95	0.92	0.92	0.95
endothelial cell	15	0.82	0.57	0.93	0.86	0.60	0.93	0.90	0.90
monocyte	6	0.00	0.00	0.60	0.50	0.59	0.62	0.60	0.67
non-classical monocyte	1	0.00	0.00	0.00	0.00	0.50	0.00	0.00	0.00
neutrophil	3	1.00	0.00	1.00	0.80	0.86	0.80	0.80	1.00
T cell	4	0.00	0.00	0.40	0.00	0.13	0.00	0.00	0.00
plasma cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
intermediate monocyte	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
kidney epithelial cell	8349	0.99	1.00	1.00	1.00	0.98	1.00	1.00	1.00
CD8-positive, alpha-beta T cell	492	0.82	0.85	0.88	0.84	0.92	1.00	1.00	0.94
B cell	446	0.97	0.89	0.97	0.97	0.98	1.00	1.00	1.00
macrophage	299	0.79	0.71	0.84	0.79	0.79	0.99	0.96	0.92
CD4-positive, alpha-beta T cell	270	0.76	0.84	0.84	0.81	0.90	1.00	1.00	0.92
natural killer cell	183	0.92	0.92	0.93	0.90	0.92	1.00	1.00	0.97
endothelial cell	86	0.78	0.39	0.95	0.89	0.53	0.99	0.82	0.96
monocyte	48	0.00	0.00	0.57	0.35	0.91	1.00	1.00	0.72
non-classical monocyte	26	0.00	0.00	0.65	0.18	0.93	1.00	1.00	0.76
neutrophil	19	1.00	0.00	0.93	0.93	0.73	1.00	1.00	1.00
T cell	13	0.00	0.00	0.00	0.00	0.27	1.00	1.00	0.63
plasma cell	5	0.00	0.00	0.00	0.00	1.00	1.00	1.00	1.00
intermediate monocyte	2	0.00	0.00	0.00	0.00	0.67	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

popV/tabula_sapiens_Kidney

Model description

Metrics

References

popV/
tabula_sapiens_Kidney