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popV/
tabula_sapiens_Trachea

Name: tabula_sapiens_Trachea
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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
basal cell	1030	0.99	0.98	0.98	0.96	0.90	0.98	0.98	0.99
neutrophil	452	0.99	0.99	0.99	0.95	0.90	0.99	0.98	0.99
fibroblast	172	0.96	0.95	0.97	0.98	0.94	0.97	0.98	0.98
CD8-positive, alpha-beta T cell	133	0.92	0.91	0.92	0.91	0.91	0.93	0.95	0.92
ciliated columnar cell of tracheobronchial tree	72	0.97	0.96	0.94	0.91	0.79	0.95	0.97	0.97
macrophage	70	0.95	0.97	0.96	0.93	0.94	0.97	0.97	0.97
B cell	67	0.98	0.98	0.98	0.98	0.98	0.99	0.99	0.99
endothelial cell	48	0.96	0.96	0.98	0.98	0.89	0.99	0.98	0.99
serous cell of epithelium of trachea	30	0.67	0.00	0.64	0.64	0.67	0.65	0.71	0.70
plasma cell	20	0.90	0.90	0.93	0.84	0.95	0.95	0.90	0.95
CD4-positive, alpha-beta T cell	33	0.83	0.66	0.77	0.71	0.78	0.81	0.88	0.79
mucus secreting cell	33	0.76	0.81	0.84	0.84	0.68	0.77	0.85	0.87
tracheal goblet cell	35	0.76	0.73	0.79	0.78	0.67	0.92	0.86	0.93
connective tissue cell	10	0.80	0.00	0.95	1.00	0.83	0.95	0.91	1.00
smooth muscle cell	15	0.78	0.80	0.76	0.88	0.82	0.80	0.85	0.80
mast cell	16	0.97	0.97	0.97	0.97	0.97	0.97	0.97	0.97
monocyte	7	0.57	0.73	0.73	0.44	0.59	0.83	0.73	0.73
natural killer cell	8	0.70	0.62	0.82	0.78	0.76	0.82	0.70	0.74
granulocyte	5	0.00	0.00	0.00	0.00	0.12	0.43	0.22	0.00
mature NK T cell	5	0.25	0.00	0.00	0.50	0.38	0.91	0.80	0.50
T cell	2	0.80	0.00	1.00	0.00	0.00	0.00	0.00	0.00
ionocyte	1	1.00	0.00	1.00	1.00	0.40	1.00	1.00	1.00
regulatory T cell	3	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
intermediate monocyte	1	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
innate lymphoid cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
plasmacytoid dendritic cell	0	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

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
basal cell	9217	0.98	0.98	0.99	0.96	0.94	0.98	0.98	0.99
neutrophil	4232	0.99	0.99	0.99	0.95	0.94	1.00	0.99	1.00
fibroblast	1628	0.95	0.94	0.96	0.97	0.96	0.99	0.99	0.99
CD8-positive, alpha-beta T cell	1069	0.91	0.92	0.92	0.91	0.94	0.98	0.98	0.95
ciliated columnar cell of tracheobronchial tree	641	0.96	0.98	0.95	0.96	0.88	0.98	0.98	0.98
macrophage	642	0.92	0.93	0.94	0.91	0.96	0.99	0.99	0.96
B cell	560	0.97	0.97	0.97	0.96	0.97	1.00	1.00	0.99
endothelial cell	538	0.98	0.98	0.98	0.96	0.96	0.99	0.99	0.99
serous cell of epithelium of trachea	296	0.72	0.07	0.87	0.82	0.83	0.76	0.80	0.93
plasma cell	272	0.97	0.98	0.98	0.93	0.99	1.00	0.99	1.00
CD4-positive, alpha-beta T cell	245	0.72	0.67	0.72	0.66	0.87	0.96	0.97	0.83
mucus secreting cell	237	0.69	0.78	0.85	0.86	0.81	0.86	0.85	0.89
tracheal goblet cell	197	0.73	0.56	0.81	0.78	0.59	0.85	0.84	0.91
connective tissue cell	142	0.75	0.00	0.86	0.95	0.83	0.96	0.97	0.98
smooth muscle cell	116	0.79	0.82	0.82	0.85	0.83	0.92	0.92	0.88
mast cell	103	0.96	0.96	0.96	0.95	0.95	1.00	1.00	0.98
monocyte	74	0.58	0.62	0.68	0.45	0.78	0.97	0.97	0.84
natural killer cell	56	0.68	0.70	0.63	0.73	0.81	0.92	0.90	0.90
granulocyte	34	0.00	0.00	0.00	0.00	0.17	0.80	0.62	0.16
mature NK T cell	32	0.29	0.21	0.30	0.46	0.45	0.93	0.96	0.82
T cell	17	0.62	0.11	0.42	0.35	0.62	1.00	1.00	0.87
ionocyte	17	0.64	0.00	0.77	0.71	0.81	1.00	1.00	0.94
regulatory T cell	14	0.00	0.00	0.00	0.00	0.82	1.00	1.00	0.73
intermediate monocyte	15	0.00	0.00	0.21	0.12	0.62	1.00	1.00	0.50
non-classical monocyte	5	0.00	0.00	0.00	0.00	0.32	1.00	1.00	0.57
innate lymphoid cell	2	0.00	0.00	0.00	0.00	0.67	1.00	1.00	1.00
plasmacytoid dendritic cell	1	0.00	0.00	0.00	0.00	0.40	1.00	1.00	1.00
myeloid dendritic cell	1	0.00	0.00	0.00	0.00	0.40	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_Trachea

Model description

Metrics

References

popV/
tabula_sapiens_Trachea