popV/tabula_sapiens_Small_Intestine

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
enterocyte of epithelium proper of duodenum	1351	0.93	0.91	0.91	0.80	0.00	0.83	0.91	0.93	0.96
enterocyte of epithelium proper of ileum	630	0.97	0.92	0.91	0.50	0.00	0.72	0.97	0.97	0.97
CD4-positive, alpha-beta T cell	532	0.88	0.88	0.91	0.83	0.00	0.76	0.88	0.87	0.93
CD8-positive, alpha-beta T cell	346	0.85	0.75	0.90	0.74	0.00	0.73	0.80	0.83	0.90
small intestine goblet cell	214	0.94	0.94	0.93	0.90	0.00	0.92	0.93	0.95	0.94
paneth cell of epithelium of small intestine	183	0.70	0.78	0.80	0.72	0.00	0.62	0.70	0.73	0.82
enterocyte of epithelium proper of small intestine	150	0.62	0.53	0.79	0.49	0.00	0.58	0.72	0.78	0.85
activated CD8-positive, alpha-beta T cell	101	0.75	0.32	0.87	0.36	0.00	0.51	0.70	0.73	0.79
BEST4+ enteroycte	78	0.81	0.84	0.86	0.83	0.00	0.86	0.81	0.81	0.88
plasma cell	77	0.97	0.98	0.99	0.99	0.00	0.97	0.99	0.99	0.99
B cell	68	0.99	0.98	0.99	0.99	0.00	0.96	0.97	0.98	0.99
intestinal crypt stem cell of small intestine	56	0.35	0.43	0.46	0.39	0.00	0.45	0.42	0.50	0.51
activated CD4-positive, alpha-beta T cell	66	0.43	0.15	0.55	0.44	0.00	0.41	0.48	0.51	0.64
fibroblast	46	1.00	0.99	0.99	0.99	0.00	0.98	0.99	0.97	0.99
intestinal tuft cell	52	1.00	1.00	1.00	0.98	0.00	0.99	1.00	1.00	1.00
enterocyte of epithelium proper of jejunum	47	0.14	0.00	0.15	0.08	0.00	0.16	0.55	0.51	0.31
macrophage	47	0.91	0.93	0.94	0.91	0.00	0.93	0.94	0.91	0.93
enteroendocrine cell of small intestine	20	0.88	0.89	0.87	0.90	0.00	0.90	0.81	0.86	0.87
mast cell	24	0.96	0.98	0.98	1.00	0.00	0.94	0.98	0.98	0.98
natural killer cell	20	0.00	0.09	0.25	0.15	0.00	0.20	0.10	0.39	0.22
enteroglial cell	20	0.95	0.95	0.95	0.98	0.00	0.89	0.95	0.95	0.98
endothelial cell of arteriole	15	0.70	0.88	0.76	0.80	0.00	0.84	0.97	0.90	0.88
gamma-delta T cell	9	0.55	0.48	0.53	0.27	0.00	0.58	0.38	0.58	0.67
naive thymus-derived CD4-positive, alpha-beta T cell	8	0.00	0.40	0.00	0.00	0.00	0.32	0.60	0.57	0.40
monocyte	8	0.82	0.80	0.77	0.59	0.00	0.80	0.74	0.78	0.80
neutrophil	4	0.40	0.67	0.60	0.86	0.00	0.43	0.89	0.75	0.67
endothelial cell of lymphatic vessel	8	1.00	1.00	1.00	0.80	0.00	0.80	1.00	1.00	1.00
endothelial cell of venule	6	0.00	0.80	0.20	0.20	0.00	0.71	0.92	0.91	0.73
myofibroblast cell	6	0.67	0.91	0.92	0.80	0.00	1.00	0.83	1.00	1.00
transit amplifying cell of small intestine	2	0.00	0.00	0.00	0.00	0.00	0.20	0.00	0.00	0.00
innate lymphoid cell	3	0.86	0.00	0.50	0.40	0.00	0.55	0.33	0.80	1.00
pericyte	4	0.67	1.00	1.00	0.75	0.00	1.00	1.00	1.00	1.00
regulatory T cell	3	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.50	0.00
myeloid dendritic 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
enterocyte of epithelium proper of duodenum	12144	0.93	0.92	0.93	0.82	0.00	0.94	0.92	0.94	0.97
enterocyte of epithelium proper of ileum	5847	0.97	0.93	0.92	0.56	0.00	0.95	0.98	0.98	0.99
CD4-positive, alpha-beta T cell	4623	0.89	0.90	0.93	0.84	0.00	0.90	0.91	0.91	0.95
CD8-positive, alpha-beta T cell	3126	0.83	0.79	0.90	0.77	0.00	0.83	0.84	0.86	0.92
small intestine goblet cell	1830	0.94	0.95	0.96	0.91	0.00	0.94	0.96	0.96	0.96
paneth cell of epithelium of small intestine	1670	0.74	0.81	0.83	0.75	0.00	0.68	0.79	0.81	0.87
enterocyte of epithelium proper of small intestine	1265	0.60	0.51	0.83	0.54	0.00	0.84	0.82	0.86	0.89
activated CD8-positive, alpha-beta T cell	1046	0.71	0.43	0.88	0.58	0.00	0.79	0.78	0.83	0.89
BEST4+ enteroycte	802	0.81	0.86	0.87	0.80	0.00	0.86	0.83	0.85	0.89
plasma cell	745	0.98	0.99	0.99	0.99	0.00	0.98	0.98	0.99	0.99
B cell	705	0.99	0.99	0.99	0.98	0.00	0.97	0.99	0.99	0.99
intestinal crypt stem cell of small intestine	531	0.36	0.47	0.46	0.36	0.00	0.54	0.67	0.72	0.69
activated CD4-positive, alpha-beta T cell	504	0.43	0.37	0.63	0.45	0.00	0.56	0.61	0.63	0.76
fibroblast	447	0.97	0.97	0.97	0.97	0.00	0.97	0.98	0.99	0.98
intestinal tuft cell	396	0.96	0.97	0.97	0.96	0.00	0.98	0.98	0.99	0.98
enterocyte of epithelium proper of jejunum	358	0.18	0.00	0.68	0.07	0.00	0.82	0.56	0.54	0.82
macrophage	319	0.88	0.91	0.89	0.90	0.00	0.97	0.99	0.98	0.95
enteroendocrine cell of small intestine	244	0.92	0.91	0.92	0.88	0.00	0.90	0.94	0.97	0.93
mast cell	226	0.95	0.96	0.96	0.97	0.00	0.95	0.98	0.98	0.97
natural killer cell	141	0.00	0.15	0.35	0.20	0.00	0.55	0.79	0.85	0.85
enteroglial cell	122	0.92	0.92	0.92	0.94	0.00	0.89	0.99	0.99	0.98
endothelial cell of arteriole	117	0.77	0.94	0.87	0.85	0.00	0.92	0.99	1.00	0.95
gamma-delta T cell	112	0.71	0.73	0.67	0.62	0.00	0.82	0.92	0.96	0.95
naive thymus-derived CD4-positive, alpha-beta T cell	107	0.00	0.42	0.09	0.25	0.00	0.71	0.85	0.87	0.74
monocyte	70	0.85	0.87	0.67	0.67	0.00	0.97	0.97	1.00	0.99
neutrophil	73	0.63	0.77	0.76	0.77	0.00	0.85	0.99	0.99	0.87
endothelial cell of lymphatic vessel	65	0.98	0.98	0.98	0.91	0.00	0.94	0.98	0.98	0.98
endothelial cell of venule	46	0.00	0.87	0.66	0.46	0.00	0.82	0.96	0.97	0.93
myofibroblast cell	45	0.75	0.94	0.94	0.85	0.00	0.89	0.95	0.95	0.95
transit amplifying cell of small intestine	32	0.00	0.00	0.46	0.00	0.00	0.63	0.75	0.90	0.86
innate lymphoid cell	31	0.64	0.63	0.60	0.43	0.00	0.78	0.93	0.98	0.91
pericyte	20	0.62	0.98	0.93	0.76	0.00	0.95	1.00	1.00	0.98
regulatory T cell	12	0.00	0.15	0.00	0.14	0.00	0.69	0.92	0.92	0.29
myeloid dendritic cell	11	0.00	0.56	0.40	0.00	0.00	0.67	1.00	1.00	0.84

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