popV/tabula_sapiens_Mammary

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
luminal epithelial cell of mammary gland	1567	0.99	0.96	1.00	0.99	0.00	0.98	0.98	0.99	0.99
fibroblast of breast	546	0.98	0.97	0.99	0.98	0.00	0.97	0.98	0.97	0.98
CD8-positive, alpha-beta T cell	237	0.88	0.88	0.89	0.84	0.00	0.84	0.88	0.91	0.92
basal cell	168	0.95	0.92	0.97	0.94	0.00	0.93	0.95	0.92	0.97
progenitor cell of mammary luminal epithelium	153	0.99	0.33	0.97	0.98	0.00	0.96	0.95	0.97	0.99
endothelial cell	171	0.98	0.98	0.98	0.96	0.00	0.95	0.97	0.97	0.98
macrophage	68	0.94	0.99	0.98	0.96	0.00	0.96	0.98	0.95	0.97
CD4-positive, alpha-beta T cell	73	0.66	0.61	0.64	0.44	0.00	0.64	0.73	0.80	0.75
vascular associated smooth muscle cell	54	0.95	0.96	0.96	0.95	0.00	0.91	0.92	0.91	0.94
plasma cell	24	0.98	1.00	0.98	0.92	0.00	0.76	0.98	0.96	0.98
T cell	21	0.57	0.12	0.44	0.00	0.00	0.46	0.57	0.56	0.57
mast cell	5	0.57	0.00	0.80	0.83	0.00	0.77	0.83	1.00	0.83
B cell	3	0.00	1.00	0.50	0.40	0.00	0.86	1.00	0.80	1.00
mature NK T cell	2	0.00	0.00	0.00	0.00	0.00	0.00	0.67	0.00	0.00
basophil	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	1.00	0.00
natural killer cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
regulatory T cell	1	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
luminal epithelial cell of mammary gland	13865	0.99	0.95	0.99	0.99	0.00	0.98	0.99	0.99	0.99
fibroblast of breast	4724	0.98	0.96	0.99	0.98	0.00	0.98	0.98	0.98	0.99
CD8-positive, alpha-beta T cell	2416	0.88	0.92	0.93	0.86	0.00	0.90	0.92	0.94	0.95
basal cell	1651	0.96	0.93	0.97	0.95	0.00	0.94	0.97	0.95	0.97
progenitor cell of mammary luminal epithelium	1541	0.99	0.40	0.98	0.99	0.00	0.96	0.97	0.98	0.99
endothelial cell	1363	0.96	0.97	0.98	0.98	0.00	0.96	0.97	0.97	0.98
macrophage	617	0.94	0.98	0.98	0.95	0.00	0.97	0.98	0.97	0.98
CD4-positive, alpha-beta T cell	608	0.65	0.71	0.72	0.46	0.00	0.73	0.82	0.85	0.86
vascular associated smooth muscle cell	512	0.95	0.96	0.96	0.95	0.00	0.92	0.94	0.92	0.96
plasma cell	269	0.98	0.97	0.97	0.89	0.00	0.80	0.99	0.98	0.99
T cell	202	0.61	0.35	0.63	0.22	0.00	0.70	0.84	0.83	0.88
mast cell	32	0.54	0.34	0.89	0.81	0.00	0.97	0.98	0.96	1.00
B cell	12	0.00	0.91	0.74	0.15	0.00	0.75	1.00	1.00	1.00
mature NK T cell	12	0.00	0.00	0.00	0.00	0.00	0.32	1.00	0.96	0.67
basophil	11	0.00	0.53	0.00	0.00	0.00	0.25	1.00	0.88	1.00
natural killer cell	6	0.00	0.00	0.00	0.00	0.00	0.27	0.92	1.00	0.00
regulatory T cell	1	0.00	0.00	0.00	0.00	0.00	0.40	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