popV/tabula_sapiens_Thymus

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
CD4-positive, alpha-beta T cell	745	0.76	0.84	0.86	0.81	0.00	0.80	0.73	0.79	0.87
CD4-positive, alpha-beta thymocyte	424	0.68	0.54	0.78	0.69	0.00	0.69	0.63	0.71	0.77
B cell	453	1.00	1.00	0.99	1.00	0.00	1.00	1.00	1.00	1.00
thymic fibroblast type 2	381	0.85	0.90	0.91	0.92	0.00	0.91	0.89	0.90	0.94
thymic fibroblast type 1	337	0.85	0.89	0.89	0.91	0.00	0.90	0.89	0.89	0.92
CD8-positive, alpha-beta T cell	290	0.80	0.87	0.87	0.84	0.00	0.85	0.84	0.87	0.88
capillary endothelial cell	275	0.82	0.86	0.90	0.85	0.00	0.84	0.85	0.84	0.88
naive thymus-derived CD4-positive, alpha-beta T cell	261	0.50	0.45	0.55	0.44	0.00	0.56	0.40	0.51	0.59
smooth muscle cell	223	0.98	0.96	0.97	0.97	0.00	0.99	0.99	0.98	0.99
vein endothelial cell	213	0.84	0.84	0.88	0.85	0.00	0.86	0.86	0.85	0.88
plasma cell	138	1.00	1.00	1.00	0.99	0.00	0.99	1.00	1.00	1.00
endothelial cell of artery	85	0.84	0.93	0.95	0.87	0.00	0.87	0.91	0.91	0.94
macrophage	87	0.97	0.98	0.99	0.98	0.00	0.98	0.99	0.98	0.99
CD8-positive, alpha-beta thymocyte	74	0.70	0.78	0.81	0.64	0.00	0.75	0.63	0.67	0.81
thymocyte	48	0.68	0.76	0.79	0.80	0.00	0.63	0.65	0.81	0.84
naive thymus-derived CD8-positive, alpha-beta T cell	38	0.58	0.54	0.54	0.00	0.00	0.55	0.47	0.59	0.66
natural killer cell	44	0.89	0.98	0.95	0.89	0.00	0.82	0.90	0.94	0.97
endothelial cell of lymphatic vessel	35	1.00	1.00	0.99	0.96	0.00	0.95	0.99	0.99	1.00
fibroblast	22	0.45	0.19	0.29	0.08	0.00	1.00	0.74	0.84	0.85
vascular associated smooth muscle cell	15	0.77	0.00	0.40	0.42	0.00	0.93	0.97	0.85	0.85
mesothelial cell	15	0.74	0.93	0.93	0.73	0.00	0.85	0.85	0.90	0.90
erythrocyte	17	0.91	0.94	0.88	0.91	0.00	0.94	0.91	0.94	0.94
neuro-medullary thymic epithelial cell	15	0.97	0.97	0.89	0.97	0.00	0.94	0.97	0.97	1.00
neutrophil	12	0.74	0.81	0.92	0.88	0.00	0.88	0.92	0.87	0.88
hematopoietic precursor cell	10	0.80	0.43	0.90	0.90	0.00	0.90	0.90	0.86	0.84
myo-medullary thymic epithelial cell	5	0.91	0.91	0.91	1.00	0.00	0.91	0.91	0.91	0.91
medullary thymic epithelial cell	7	1.00	1.00	0.92	0.67	0.00	0.86	1.00	1.00	1.00
monocyte	1	0.00	0.00	1.00	0.00	0.00	0.00	1.00	0.00	0.00
mast cell	3	0.00	1.00	1.00	0.50	0.00	0.57	1.00	1.00	1.00
fast muscle cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
T follicular helper cell	0	0.00	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	0.00
endothelial cell	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
CD4-positive, alpha-beta T cell	6381	0.76	0.84	0.87	0.82	0.00	0.82	0.74	0.78	0.87
CD4-positive, alpha-beta thymocyte	4139	0.72	0.53	0.82	0.75	0.00	0.76	0.69	0.75	0.81
B cell	4009	1.00	1.00	1.00	1.00	0.00	1.00	1.00	1.00	1.00
thymic fibroblast type 2	3824	0.87	0.91	0.93	0.93	0.00	0.92	0.92	0.92	0.94
thymic fibroblast type 1	2933	0.84	0.89	0.91	0.89	0.00	0.90	0.90	0.90	0.92
CD8-positive, alpha-beta T cell	2527	0.78	0.85	0.87	0.84	0.00	0.85	0.82	0.84	0.87
capillary endothelial cell	2346	0.82	0.87	0.92	0.89	0.00	0.88	0.89	0.88	0.91
naive thymus-derived CD4-positive, alpha-beta T cell	2262	0.49	0.45	0.60	0.54	0.00	0.60	0.50	0.57	0.65
smooth muscle cell	2002	0.96	0.95	0.99	0.96	0.00	1.00	0.99	0.99	0.99
vein endothelial cell	1835	0.83	0.84	0.91	0.87	0.00	0.88	0.89	0.88	0.91
plasma cell	1440	0.99	0.99	0.99	0.99	0.00	0.99	1.00	1.00	1.00
endothelial cell of artery	688	0.87	0.94	0.95	0.91	0.00	0.90	0.95	0.94	0.96
macrophage	683	0.97	0.98	0.98	0.97	0.00	0.99	1.00	0.99	0.99
CD8-positive, alpha-beta thymocyte	598	0.65	0.76	0.79	0.60	0.00	0.79	0.76	0.81	0.84
thymocyte	407	0.68	0.71	0.80	0.74	0.00	0.73	0.83	0.87	0.91
naive thymus-derived CD8-positive, alpha-beta T cell	396	0.57	0.54	0.66	0.13	0.00	0.68	0.68	0.74	0.79
natural killer cell	384	0.88	0.92	0.92	0.86	0.00	0.87	0.95	0.95	0.96
endothelial cell of lymphatic vessel	336	0.97	0.98	0.97	0.96	0.00	0.96	0.99	0.98	0.99
fibroblast	250	0.65	0.31	0.90	0.29	0.00	0.99	0.86	0.91	0.95
vascular associated smooth muscle cell	226	0.66	0.14	0.94	0.49	0.00	0.97	0.97	0.96	0.97
mesothelial cell	160	0.87	0.94	0.95	0.91	0.00	0.96	0.97	0.98	0.97
erythrocyte	135	0.93	0.93	0.92	0.94	0.00	0.94	0.94	0.95	0.97
neuro-medullary thymic epithelial cell	120	0.92	0.94	0.87	0.87	0.00	0.95	1.00	0.98	0.95
neutrophil	109	0.62	0.76	0.89	0.86	0.00	0.98	0.98	0.99	1.00
hematopoietic precursor cell	82	0.74	0.36	0.87	0.86	0.00	0.96	0.99	0.99	0.99
myo-medullary thymic epithelial cell	72	0.85	0.85	0.95	0.88	0.00	0.99	0.97	0.99	0.97
medullary thymic epithelial cell	36	0.84	0.79	0.80	0.68	0.00	0.99	1.00	1.00	0.92
monocyte	25	0.41	0.00	0.76	0.44	0.00	0.85	0.98	0.98	0.89
mast cell	21	0.00	0.89	0.76	0.50	0.00	0.79	1.00	1.00	0.98
fast muscle cell	21	0.00	0.09	0.95	0.38	0.00	0.95	1.00	1.00	0.98
T follicular helper cell	6	0.00	0.00	0.00	0.00	0.00	0.29	0.75	0.75	0.83
innate lymphoid cell	2	0.00	0.00	0.00	0.00	0.00	0.29	0.80	0.80	1.00
endothelial cell	1	0.00	0.00	0.00	0.00	0.00	0.29	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