popV/tabula_sapiens_Bone_Marrow

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	857	0.96	0.96	0.97	0.96	0.00	0.88	0.95	0.95	0.98
CD4-positive, alpha-beta T cell	304	0.86	0.87	0.87	0.84	0.00	0.86	0.88	0.91	0.89
CD8-positive, alpha-beta T cell	242	0.82	0.83	0.83	0.78	0.00	0.82	0.84	0.87	0.84
monocyte	212	0.70	0.79	0.82	0.75	0.00	0.74	0.66	0.76	0.80
B cell	189	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.98	0.99
hematopoietic precursor cell	177	0.79	0.85	0.84	0.80	0.00	0.85	0.85	0.86	0.86
plasma cell	152	0.98	0.99	1.00	0.99	0.00	0.99	0.99	0.99	1.00
natural killer cell	100	0.91	0.93	0.93	0.92	0.00	0.90	0.96	0.94	0.93
erythroid progenitor cell	107	0.77	0.77	0.77	0.80	0.00	0.78	0.82	0.85	0.84
hematopoietic stem cell	82	0.80	0.83	0.87	0.80	0.00	0.82	0.85	0.87	0.89
granulocyte	73	0.71	0.40	0.69	0.12	0.00	0.39	0.64	0.68	0.79
erythrocyte	44	0.67	0.62	0.64	0.63	0.00	0.60	0.77	0.77	0.68
common myeloid progenitor	45	0.69	0.73	0.66	0.72	0.00	0.76	0.72	0.80	0.77
macrophage	32	0.57	0.49	0.61	0.40	0.00	0.58	0.67	0.65	0.69
classical monocyte	27	0.20	0.00	0.07	0.07	0.00	0.28	0.20	0.33	0.06
intermediate monocyte	23	0.39	0.46	0.40	0.30	0.00	0.46	0.33	0.43	0.48
myeloid dendritic cell	11	0.57	0.44	0.63	0.76	0.00	0.62	0.50	0.69	0.80
T cell	12	0.64	0.40	0.53	0.27	0.00	0.53	0.76	0.71	0.80
mature NK T cell	9	0.00	0.71	0.00	0.00	0.00	0.30	0.80	0.67	0.50
non-classical monocyte	8	0.00	0.22	0.00	0.00	0.00	0.15	0.00	0.17	0.00
basophil	1	0.00	0.00	0.00	0.00	0.00	0.29	0.00	0.00	0.00
regulatory T cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
fibroblast	1	0.00	0.00	0.00	1.00	0.00	0.00	0.00	0.00	0.00
plasmacytoid dendritic cell	4	0.00	0.00	0.00	0.00	0.00	0.73	0.00	0.33	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
neutrophil	7820	0.97	0.97	0.97	0.96	0.00	0.95	0.96	0.96	0.98
CD4-positive, alpha-beta T cell	2869	0.85	0.87	0.87	0.86	0.00	0.86	0.89	0.91	0.89
CD8-positive, alpha-beta T cell	2394	0.83	0.86	0.86	0.81	0.00	0.83	0.86	0.88	0.87
monocyte	1828	0.77	0.82	0.84	0.81	0.00	0.81	0.81	0.85	0.88
B cell	1630	0.99	0.99	0.99	0.99	0.00	0.99	0.99	0.99	0.99
hematopoietic precursor cell	1543	0.80	0.87	0.89	0.84	0.00	0.90	0.88	0.90	0.92
plasma cell	1296	0.98	0.99	0.99	0.99	0.00	0.99	0.99	1.00	0.99
natural killer cell	999	0.92	0.95	0.95	0.91	0.00	0.94	0.96	0.96	0.97
erythroid progenitor cell	864	0.73	0.79	0.77	0.78	0.00	0.89	0.92	0.95	0.93
hematopoietic stem cell	710	0.76	0.86	0.87	0.81	0.00	0.89	0.95	0.94	0.92
granulocyte	562	0.71	0.26	0.71	0.26	0.00	0.58	0.71	0.69	0.83
erythrocyte	409	0.71	0.72	0.72	0.70	0.00	0.90	0.94	0.95	0.90
common myeloid progenitor	408	0.67	0.74	0.69	0.71	0.00	0.85	0.92	0.95	0.92
macrophage	326	0.62	0.59	0.69	0.58	0.00	0.83	0.89	0.92	0.91
classical monocyte	204	0.23	0.00	0.08	0.17	0.00	0.54	0.72	0.76	0.66
intermediate monocyte	201	0.47	0.54	0.58	0.49	0.00	0.78	0.87	0.95	0.82
myeloid dendritic cell	97	0.50	0.54	0.65	0.60	0.00	0.78	0.82	0.82	0.85
T cell	86	0.47	0.30	0.48	0.49	0.00	0.46	0.67	0.65	0.70
mature NK T cell	55	0.00	0.45	0.19	0.14	0.00	0.59	0.92	0.92	0.93
non-classical monocyte	45	0.00	0.40	0.27	0.28	0.00	0.85	0.94	0.94	0.84
basophil	22	0.00	0.37	0.53	0.55	0.00	0.46	0.88	0.79	0.82
regulatory T cell	14	0.00	0.00	0.00	0.00	0.00	0.65	0.76	0.70	0.44
fibroblast	10	0.00	0.33	0.38	0.47	0.00	0.50	0.83	0.87	0.80
plasmacytoid dendritic cell	5	0.00	0.00	0.00	0.00	0.00	0.24	1.00	0.83	1.00
endothelial cell	3	0.00	0.00	0.00	0.00	0.00	1.00	1.00	1.00	0.50

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