popV/tabula_sapiens_Fat

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
fibroblast	2663	0.90	0.92	0.95	0.95	0.00	0.87	0.88	0.90	0.94
macrophage	1561	0.91	0.93	0.95	0.94	0.00	0.88	0.91	0.91	0.94
B cell	1443	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
CD4-positive, alpha-beta T cell	1129	0.88	0.89	0.90	0.88	0.00	0.83	0.84	0.88	0.90
endothelial cell	628	0.96	0.97	0.98	0.97	0.00	0.96	0.97	0.96	0.97
CD8-positive, alpha-beta T cell	534	0.76	0.76	0.77	0.72	0.00	0.71	0.73	0.78	0.80
mesenchymal stem cell of adipose tissue	391	0.51	0.11	0.64	0.61	0.00	0.49	0.49	0.54	0.65
neutrophil	293	0.96	0.96	0.97	0.96	0.00	0.97	0.95	0.96	0.97
smooth muscle cell	220	0.81	0.87	0.91	0.85	0.00	0.83	0.88	0.90	0.91
myofibroblast cell	130	0.79	0.83	0.88	0.77	0.00	0.81	0.89	0.90	0.89
natural killer cell	72	0.82	0.82	0.83	0.81	0.00	0.76	0.78	0.78	0.85
pericyte	101	0.84	0.83	0.91	0.90	0.00	0.77	0.79	0.84	0.89
monocyte	81	0.63	0.75	0.80	0.75	0.00	0.57	0.69	0.69	0.79
mature NK T cell	41	0.78	0.75	0.74	0.61	0.00	0.71	0.65	0.72	0.78
T cell	33	0.40	0.43	0.59	0.57	0.00	0.32	0.24	0.36	0.46
plasma cell	37	0.80	0.87	0.89	0.89	0.00	0.77	0.94	0.86	0.92
erythrocyte	26	0.93	0.94	0.96	0.90	0.00	0.92	0.95	1.00	0.98
muscle cell	22	0.94	0.93	0.98	0.98	0.00	0.96	0.94	0.92	0.94
leukocyte	16	0.65	0.73	0.65	0.40	0.00	0.39	0.54	0.51	0.73
mast cell	8	0.76	0.94	0.94	0.94	0.00	0.76	0.84	0.89	0.94
hematopoietic precursor cell	7	0.36	0.00	0.60	0.60	0.00	0.50	0.52	0.71	0.80
intermediate monocyte	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
mesenchymal stem cell	1	0.00	0.00	0.00	0.00	0.00	0.00	1.00	0.00	0.00
myeloid dendritic cell	3	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
classical monocyte	1	0.00	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	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	0.00
platelet	0	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
fibroblast	23306	0.91	0.92	0.96	0.96	0.00	0.89	0.89	0.92	0.95
macrophage	13692	0.92	0.94	0.96	0.95	0.00	0.89	0.92	0.92	0.94
B cell	13326	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
CD4-positive, alpha-beta T cell	10352	0.88	0.91	0.91	0.90	0.00	0.87	0.87	0.89	0.91
endothelial cell	6338	0.97	0.98	0.98	0.97	0.00	0.97	0.97	0.97	0.98
CD8-positive, alpha-beta T cell	4668	0.75	0.79	0.80	0.75	0.00	0.74	0.76	0.80	0.81
mesenchymal stem cell of adipose tissue	3386	0.52	0.13	0.72	0.69	0.00	0.53	0.51	0.59	0.69
neutrophil	3086	0.97	0.97	0.98	0.97	0.00	0.98	0.97	0.97	0.98
smooth muscle cell	1740	0.86	0.87	0.95	0.87	0.00	0.91	0.91	0.93	0.95
myofibroblast cell	936	0.84	0.82	0.93	0.77	0.00	0.89	0.91	0.91	0.94
natural killer cell	801	0.85	0.86	0.87	0.83	0.00	0.85	0.89	0.90	0.90
pericyte	763	0.82	0.83	0.93	0.92	0.00	0.73	0.79	0.83	0.86
monocyte	760	0.65	0.79	0.82	0.78	0.00	0.59	0.72	0.72	0.77
mature NK T cell	337	0.73	0.79	0.78	0.62	0.00	0.78	0.82	0.84	0.87
T cell	298	0.41	0.44	0.58	0.57	0.00	0.37	0.42	0.45	0.58
plasma cell	276	0.81	0.91	0.93	0.92	0.00	0.79	0.93	0.85	0.93
erythrocyte	256	0.95	0.94	0.97	0.94	0.00	0.95	0.98	0.97	0.99
muscle cell	241	0.98	0.86	0.99	0.99	0.00	0.98	0.96	0.98	0.99
leukocyte	152	0.69	0.75	0.72	0.41	0.00	0.67	0.67	0.67	0.81
mast cell	127	0.84	0.92	0.93	0.90	0.00	0.86	0.91	0.92	0.92
hematopoietic precursor cell	67	0.39	0.00	0.59	0.59	0.00	0.56	0.71	0.69	0.86
intermediate monocyte	42	0.00	0.00	0.00	0.00	0.00	0.19	0.60	0.67	0.75
mesenchymal stem cell	16	0.00	0.00	0.00	0.00	0.00	0.06	0.76	0.89	0.48
myeloid dendritic cell	3	0.00	0.00	0.00	0.00	0.00	0.07	1.00	1.00	0.50
classical monocyte	1	0.00	0.00	0.00	0.00	0.00	0.22	1.00	1.00	0.00
non-classical monocyte	1	0.00	0.00	0.00	0.00	0.00	0.00	1.00	1.00	0.00
activated CD4-positive, alpha-beta T cell	1	0.00	0.00	0.00	0.00	0.00	0.08	1.00	1.00	1.00
platelet	1	0.00	0.00	0.00	0.00	0.00	0.20	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