popV/tabula_sapiens_Spleen

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
B cell	1667	0.99	0.99	0.99	0.99	0.00	0.98	0.99	0.99	1.00
neutrophil	1506	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
CD8-positive, alpha-beta T cell	1082	0.85	0.92	0.93	0.91	0.00	0.81	0.78	0.83	0.90
classical monocyte	469	0.82	0.87	0.86	0.85	0.00	0.79	0.78	0.84	0.87
plasma cell	387	0.98	0.99	0.99	0.99	0.00	0.99	0.99	0.99	1.00
natural killer cell	387	0.93	0.95	0.95	0.95	0.00	0.95	0.92	0.93	0.94
monocyte	324	0.69	0.75	0.76	0.75	0.00	0.69	0.57	0.71	0.77
macrophage	301	0.90	0.93	0.93	0.93	0.00	0.90	0.91	0.93	0.93
CD4-positive, alpha-beta T cell	232	0.46	0.56	0.57	0.47	0.00	0.38	0.40	0.52	0.58
naive thymus-derived CD4-positive, alpha-beta T cell	221	0.70	0.65	0.74	0.66	0.00	0.69	0.65	0.73	0.77
endothelial cell	136	0.97	0.97	0.97	0.96	0.00	0.96	0.97	0.97	0.98
mature NK T cell	106	0.75	0.78	0.80	0.78	0.00	0.75	0.64	0.74	0.79
naive thymus-derived CD8-positive, alpha-beta T cell	67	0.49	0.32	0.66	0.53	0.00	0.54	0.43	0.49	0.59
erythrocyte	43	0.94	0.97	0.98	0.99	0.00	0.95	0.95	0.87	0.98
intermediate monocyte	33	0.27	0.00	0.10	0.05	0.00	0.25	0.17	0.30	0.33
regulatory T cell	28	0.46	0.42	0.57	0.38	0.00	0.39	0.52	0.51	0.64
innate lymphoid cell	13	0.67	0.80	0.75	0.90	0.00	0.72	0.70	0.68	0.74
T cell	17	0.79	0.79	0.80	0.80	0.00	0.52	0.63	0.63	0.83
non-classical monocyte	13	0.00	0.14	0.27	0.00	0.00	0.25	0.47	0.58	0.38
hematopoietic precursor cell	6	0.43	0.73	0.55	0.73	0.00	0.77	0.77	0.67	0.83
platelet	6	0.55	0.44	0.36	0.71	0.00	0.44	0.55	0.62	0.71
myeloid dendritic cell	1	0.00	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	0.00
basophil	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
hematopoietic stem cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
fibroblast	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
B cell	14890	0.99	0.99	0.99	0.99	0.00	0.98	0.99	0.99	1.00
neutrophil	13395	0.99	1.00	0.99	0.99	0.00	0.99	0.99	0.99	1.00
CD8-positive, alpha-beta T cell	9805	0.85	0.92	0.94	0.92	0.00	0.83	0.79	0.85	0.92
classical monocyte	3993	0.82	0.87	0.87	0.86	0.00	0.82	0.83	0.86	0.89
plasma cell	3589	0.99	0.98	0.99	0.99	0.00	0.99	0.99	0.99	0.99
natural killer cell	3557	0.92	0.95	0.96	0.96	0.00	0.95	0.94	0.94	0.96
monocyte	2790	0.68	0.76	0.79	0.75	0.00	0.75	0.70	0.76	0.81
macrophage	2505	0.92	0.94	0.95	0.93	0.00	0.93	0.93	0.94	0.95
CD4-positive, alpha-beta T cell	2510	0.43	0.63	0.63	0.56	0.00	0.45	0.52	0.62	0.66
naive thymus-derived CD4-positive, alpha-beta T cell	2096	0.66	0.67	0.76	0.68	0.00	0.72	0.70	0.76	0.79
endothelial cell	1214	0.98	0.98	0.98	0.97	0.00	0.97	0.98	0.98	0.98
mature NK T cell	923	0.73	0.79	0.82	0.80	0.00	0.77	0.67	0.74	0.84
naive thymus-derived CD8-positive, alpha-beta T cell	555	0.46	0.31	0.70	0.56	0.00	0.55	0.52	0.54	0.64
erythrocyte	363	0.91	0.96	0.97	0.97	0.00	0.96	0.96	0.88	0.98
intermediate monocyte	363	0.26	0.12	0.15	0.05	0.00	0.44	0.48	0.49	0.59
regulatory T cell	314	0.46	0.53	0.60	0.46	0.00	0.53	0.61	0.65	0.72
innate lymphoid cell	157	0.74	0.87	0.87	0.83	0.00	0.77	0.79	0.89	0.88
T cell	134	0.66	0.64	0.73	0.68	0.00	0.47	0.69	0.63	0.71
non-classical monocyte	113	0.00	0.07	0.27	0.18	0.00	0.33	0.66	0.75	0.57
hematopoietic precursor cell	62	0.56	0.78	0.77	0.76	0.00	0.78	0.81	0.83	0.85
platelet	48	0.35	0.66	0.63	0.79	0.00	0.40	0.93	0.79	0.91
myeloid dendritic cell	16	0.00	0.00	0.41	0.00	0.00	0.16	0.84	0.91	0.93
plasmacytoid dendritic cell	6	0.00	0.00	0.00	0.00	0.00	0.27	1.00	1.00	1.00
basophil	2	0.00	0.00	0.00	0.00	0.00	0.06	0.57	1.00	1.00
hematopoietic stem cell	2	0.00	0.00	0.00	0.00	0.00	0.19	1.00	0.80	0.00
fibroblast	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