popV/tabula_sapiens_Large_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 of large intestine	469	0.92	0.92	0.91	0.85	0.00	0.85	0.90	0.92	0.94
CD4-positive, alpha-beta T cell	411	0.84	0.88	0.88	0.83	0.00	0.78	0.85	0.87	0.90
plasma cell	314	0.99	0.98	0.97	0.96	0.00	0.96	0.98	0.99	0.99
CD8-positive, alpha-beta T cell	288	0.77	0.85	0.84	0.68	0.00	0.75	0.80	0.82	0.85
fibroblast	251	0.96	0.98	0.97	0.97	0.00	0.96	0.98	0.98	0.98
B cell	222	0.98	0.99	0.98	0.97	0.00	0.98	0.98	0.98	0.99
gamma-delta T cell	194	0.88	0.92	0.91	0.75	0.00	0.83	0.89	0.89	0.92
intestinal crypt stem cell of colon	158	0.83	0.82	0.85	0.79	0.00	0.81	0.81	0.87	0.88
large intestine goblet cell	169	0.90	0.94	0.94	0.88	0.00	0.90	0.92	0.91	0.92
BEST4+ enteroycte	122	0.88	0.89	0.93	0.80	0.00	0.85	0.91	0.92	0.92
enteroglial cell	76	0.99	0.99	0.98	0.95	0.00	0.98	0.99	0.99	0.99
regulatory T cell	64	0.66	0.63	0.67	0.44	0.00	0.56	0.64	0.68	0.72
mast cell	48	0.98	0.98	0.98	0.98	0.00	0.98	0.98	0.96	0.98
myeloid leukocyte	30	0.86	0.88	0.93	0.92	0.00	0.88	0.91	0.97	0.95
colon endothelial cell	39	0.96	0.95	0.99	0.94	0.00	0.93	0.99	0.97	1.00
colon macrophage	38	0.83	0.83	0.87	0.88	0.00	0.83	0.90	0.89	0.92
transit amplifying cell of colon	22	0.73	0.57	0.67	0.38	0.00	0.58	0.68	0.71	0.72
naive thymus-derived CD4-positive, alpha-beta T cell	25	0.77	0.63	0.74	0.49	0.00	0.66	0.62	0.75	0.79
paneth cell of colon	22	0.54	0.41	0.60	0.65	0.00	0.67	0.77	0.84	0.82
tuft cell of colon	15	1.00	0.97	1.00	0.90	0.00	0.88	1.00	1.00	1.00
myofibroblast cell	12	0.80	0.92	0.96	1.00	0.00	0.89	0.96	0.88	0.92
monocyte	3	0.80	0.80	0.57	0.67	0.00	0.67	0.80	0.67	0.80
mature NK T cell	4	0.00	0.00	0.00	0.00	0.00	0.67	0.60	0.50	0.00
type L enteroendocrine cell	4	0.62	0.80	0.67	0.75	0.00	0.67	0.89	0.89	0.89
myeloid dendritic cell	2	0.00	0.00	0.00	0.00	0.00	0.29	0.50	0.00	0.00
enterochromaffin-like cell	4	0.00	0.86	0.00	0.33	0.00	0.86	1.00	1.00	1.00
natural killer cell	1	0.00	0.00	0.00	0.00	0.00	0.20	0.00	0.00	0.00
innate lymphoid cell	2	0.00	0.00	0.00	0.00	0.00	0.29	0.00	0.50	0.00
neutrophil	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 of large intestine	4098	0.93	0.93	0.93	0.89	0.00	0.87	0.93	0.95	0.96
CD4-positive, alpha-beta T cell	3829	0.85	0.89	0.90	0.85	0.00	0.83	0.87	0.90	0.91
plasma cell	2994	0.98	0.98	0.98	0.96	0.00	0.97	0.99	0.99	0.99
CD8-positive, alpha-beta T cell	2674	0.79	0.86	0.85	0.74	0.00	0.81	0.84	0.87	0.87
fibroblast	2346	0.98	0.98	0.98	0.97	0.00	0.97	0.99	0.99	0.98
B cell	1847	0.98	0.99	0.99	0.97	0.00	0.98	0.99	0.99	0.99
gamma-delta T cell	1662	0.90	0.93	0.93	0.79	0.00	0.87	0.92	0.93	0.94
intestinal crypt stem cell of colon	1574	0.84	0.86	0.89	0.86	0.00	0.82	0.90	0.92	0.93
large intestine goblet cell	1388	0.93	0.94	0.95	0.91	0.00	0.93	0.95	0.96	0.96
BEST4+ enteroycte	968	0.88	0.92	0.94	0.84	0.00	0.87	0.94	0.94	0.94
enteroglial cell	772	0.99	0.98	0.98	0.97	0.00	0.98	0.99	0.99	0.99
regulatory T cell	569	0.73	0.74	0.77	0.53	0.00	0.67	0.80	0.83	0.89
mast cell	345	0.97	0.97	0.98	0.96	0.00	0.97	0.99	0.98	0.99
myeloid leukocyte	324	0.87	0.91	0.91	0.93	0.00	0.96	1.00	1.00	0.98
colon endothelial cell	309	0.90	0.88	0.91	0.90	0.00	0.91	0.97	0.96	0.93
colon macrophage	290	0.81	0.86	0.86	0.88	0.00	0.95	1.00	0.99	0.94
transit amplifying cell of colon	215	0.72	0.69	0.72	0.53	0.00	0.60	0.85	0.82	0.83
naive thymus-derived CD4-positive, alpha-beta T cell	203	0.71	0.68	0.73	0.42	0.00	0.66	0.84	0.85	0.83
paneth cell of colon	195	0.61	0.35	0.74	0.72	0.00	0.74	0.90	0.94	0.91
tuft cell of colon	163	0.93	0.95	0.93	0.93	0.00	0.95	0.96	0.96	0.96
myofibroblast cell	70	0.83	0.81	0.85	0.88	0.00	0.88	1.00	0.99	0.92
monocyte	63	0.77	0.79	0.74	0.73	0.00	0.93	0.98	0.99	0.91
mature NK T cell	43	0.00	0.49	0.24	0.33	0.00	0.85	0.97	0.99	0.75
type L enteroendocrine cell	40	0.76	0.84	0.87	0.68	0.00	0.78	1.00	0.99	0.95
myeloid dendritic cell	38	0.00	0.15	0.26	0.26	0.00	0.82	1.00	1.00	0.57
enterochromaffin-like cell	23	0.00	0.63	0.77	0.65	0.00	0.74	0.96	0.98	0.93
natural killer cell	13	0.00	0.00	0.00	0.00	0.00	0.49	0.96	0.93	1.00
innate lymphoid cell	11	0.00	0.00	0.00	0.00	0.00	0.76	1.00	1.00	0.43
neutrophil	9	0.00	0.00	0.00	0.20	0.00	0.90	1.00	0.95	0.94

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