popV/tabula_sapiens_Blood

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
neutrophil	3212	0.99	0.99	0.98	0.99	0.00	0.97	0.99	0.99	1.00
erythrocyte	1173	1.00	1.00	0.98	0.99	0.00	0.99	0.99	0.99	1.00
classical monocyte	1092	0.79	0.67	0.84	0.70	0.00	0.69	0.65	0.77	0.84
monocyte	962	0.81	0.28	0.82	0.55	0.00	0.47	0.67	0.80	0.81
CD4-positive, alpha-beta T cell	472	0.84	0.89	0.89	0.89	0.00	0.72	0.78	0.85	0.88
CD8-positive, alpha-beta T cell	424	0.58	0.65	0.66	0.66	0.00	0.63	0.60	0.61	0.64
B cell	378	0.98	0.98	0.98	0.98	0.00	0.99	0.97	0.98	0.98
natural killer cell	315	0.71	0.64	0.63	0.58	0.00	0.64	0.61	0.65	0.69
macrophage	123	0.50	0.49	0.48	0.48	0.00	0.35	0.29	0.42	0.50
intermediate monocyte	86	0.46	0.02	0.64	0.13	0.00	0.32	0.38	0.42	0.61
plasma cell	85	0.98	0.98	0.95	0.97	0.00	0.95	0.93	0.97	0.98
naive thymus-derived CD4-positive, alpha-beta T cell	59	0.45	0.32	0.38	0.18	0.00	0.33	0.45	0.59	0.51
platelet	48	0.97	0.97	0.91	1.00	0.00	0.92	0.95	0.96	0.98
non-classical monocyte	44	0.72	0.72	0.70	0.41	0.00	0.73	0.73	0.76	0.77
mature NK T cell	15	0.57	0.64	0.55	0.57	0.00	0.45	0.39	0.51	0.61
hematopoietic precursor cell	11	0.69	0.72	0.58	0.72	0.00	0.39	0.64	0.64	0.80
hematopoietic stem cell	6	0.00	0.44	0.25	0.60	0.00	0.43	0.50	0.36	0.50
basophil	9	0.80	0.00	0.80	0.80	0.00	0.15	0.50	0.75	0.80
regulatory T cell	7	0.00	0.25	0.00	0.00	0.00	0.42	0.43	0.55	0.00
plasmacytoid dendritic cell	2	0.67	0.50	0.50	0.67	0.00	0.15	0.25	0.50	0.50
common myeloid progenitor	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
myeloid dendritic 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
neutrophil	28986	1.00	1.00	0.99	0.99	0.00	0.98	0.99	0.99	1.00
erythrocyte	10375	1.00	0.99	0.99	1.00	0.00	0.99	0.99	0.99	1.00
classical monocyte	9499	0.76	0.66	0.85	0.77	0.00	0.78	0.67	0.77	0.85
monocyte	8640	0.79	0.30	0.86	0.77	0.00	0.82	0.71	0.81	0.87
CD4-positive, alpha-beta T cell	4428	0.85	0.90	0.91	0.91	0.00	0.86	0.82	0.88	0.93
CD8-positive, alpha-beta T cell	4148	0.57	0.72	0.71	0.73	0.00	0.65	0.65	0.69	0.72
B cell	3515	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
natural killer cell	2742	0.69	0.69	0.67	0.66	0.00	0.68	0.64	0.69	0.73
macrophage	1105	0.49	0.47	0.50	0.50	0.00	0.44	0.41	0.54	0.60
intermediate monocyte	950	0.51	0.01	0.65	0.35	0.00	0.48	0.47	0.54	0.69
plasma cell	731	0.98	0.97	0.96	0.97	0.00	0.96	0.97	0.97	0.99
naive thymus-derived CD4-positive, alpha-beta T cell	431	0.39	0.35	0.46	0.32	0.00	0.54	0.50	0.62	0.63
platelet	390	0.92	0.96	0.94	0.99	0.00	0.85	0.96	0.97	0.98
non-classical monocyte	309	0.77	0.80	0.82	0.48	0.00	0.65	0.79	0.81	0.86
mature NK T cell	187	0.67	0.76	0.74	0.65	0.00	0.64	0.68	0.76	0.81
hematopoietic precursor cell	120	0.53	0.75	0.68	0.80	0.00	0.58	0.89	0.94	0.92
hematopoietic stem cell	58	0.00	0.50	0.57	0.65	0.00	0.79	0.96	1.00	0.91
basophil	32	0.79	0.06	0.77	0.67	0.00	0.07	0.64	0.78	0.90
regulatory T cell	33	0.00	0.06	0.34	0.00	0.00	0.35	0.67	0.67	0.39
plasmacytoid dendritic cell	27	0.68	0.78	0.80	0.78	0.00	0.30	0.89	0.90	0.91
common myeloid progenitor	3	0.00	0.00	0.00	0.00	0.00	0.04	1.00	1.00	1.00
myeloid dendritic cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	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