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	scanvi	svm	xgboost	Consensus Prediction
basal cell	3410	0.87	0.81	0.89	0.80	0.68	0.85	0.86	0.94
bladder urothelial cell	2627	0.99	0.93	0.90	0.75	0.43	0.99	0.99	0.99
luminal epithelial cell of mammary gland	1547	0.99	0.29	0.97	0.70	0.45	0.98	0.98	1.00
enterocyte of epithelium proper of duodenum	1347	0.93	0.53	0.83	0.60	0.44	0.91	0.90	0.95
stratified squamous epithelial cell	1245	0.84	0.81	0.91	0.84	0.75	0.84	0.85	0.90
acinar cell of salivary gland	1210	0.95	0.89	0.92	0.74	0.50	0.96	0.94	0.97
pulmonary alveolar type 2 cell	1160	0.97	0.98	0.97	0.96	0.81	0.97	0.97	0.98
conjunctival epithelial cell	1065	0.94	0.71	0.83	0.55	0.44	0.96	0.94	0.95
luminal cell of prostate epithelium	1075	0.92	0.80	0.92	0.68	0.10	0.95	0.95	0.95
kidney epithelial cell	926	0.99	0.86	0.93	0.54	0.30	1.00	1.00	1.00
hepatocyte	733	1.00	1.00	0.97	0.81	0.48	1.00	1.00	1.00
enterocyte of epithelium proper of ileum	693	0.98	0.13	0.83	0.45	0.15	0.98	0.98	0.98
pancreatic acinar cell	545	0.96	0.76	0.95	0.60	0.31	0.98	0.97	0.98
enterocyte of epithelium of large intestine	436	0.86	0.36	0.64	0.44	0.37	0.89	0.89	0.89
corneal epithelial cell	414	0.93	0.00	0.93	0.85	0.78	0.96	0.94	0.95
duct epithelial cell	387	0.81	0.65	0.81	0.58	0.45	0.86	0.81	0.89
basal cell of prostate epithelium	328	0.76	0.02	0.87	0.54	0.26	0.85	0.83	0.86
pulmonary alveolar type 1 cell	350	0.98	0.97	0.97	0.85	0.88	0.98	0.96	0.99
pancreatic ductal cell	264	0.94	0.14	0.91	0.75	0.62	0.96	0.94	0.96
small intestine goblet cell	188	0.91	0.85	0.87	0.59	0.50	0.92	0.91	0.95
BEST4+ enteroycte	188	0.80	0.79	0.82	0.64	0.26	0.88	0.89	0.87
paneth cell of epithelium of small intestine	185	0.68	0.59	0.75	0.37	0.46	0.65	0.66	0.81
club cell	163	0.69	0.76	0.85	0.78	0.76	0.81	0.79	0.88
intestinal crypt stem cell of colon	173	0.75	0.54	0.68	0.56	0.49	0.82	0.83	0.85
progenitor cell of mammary luminal epithelium	172	0.99	0.00	0.99	0.97	0.67	0.87	0.91	0.99
epithelial cell	159	0.97	0.91	0.90	0.60	0.36	0.98	0.98	0.97
large intestine goblet cell	155	0.90	0.76	0.79	0.52	0.55	0.92	0.91	0.92
epithelial cell of uterus	150	0.98	0.46	0.82	0.42	0.30	0.98	0.96	0.99
enterocyte of epithelium proper of small intestine	151	0.41	0.00	0.24	0.31	0.26	0.62	0.70	0.69
acinar cell	134	0.88	0.61	0.51	0.74	0.53	0.93	0.93	0.92
lung ciliated cell	134	0.74	0.60	0.80	0.64	0.75	0.96	0.93	0.94
respiratory goblet cell	119	0.31	0.51	0.82	0.50	0.52	0.61	0.60	0.76
salivary gland cell	100	0.68	0.04	0.82	0.52	0.41	0.81	0.78	0.89
ciliated columnar cell of tracheobronchial tree	75	0.31	0.30	0.72	0.57	0.54	0.92	0.91	0.90
intrahepatic cholangiocyte	50	0.99	0.19	0.70	0.56	0.36	0.99	0.95	0.96
blood vessel smooth muscle cell	59	1.00	0.71	0.96	0.89	0.85	1.00	0.97	1.00
intestinal crypt stem cell of small intestine	54	0.15	0.18	0.21	0.07	0.15	0.39	0.41	0.47
myoepithelial cell	58	0.83	0.45	0.94	0.80	0.61	0.71	0.64	0.91
intestinal tuft cell	37	0.75	0.79	0.89	0.76	0.70	0.95	0.93	0.88
enterocyte of epithelium proper of jejunum	43	0.23	0.00	0.49	0.17	0.03	0.53	0.43	0.68
serous cell of epithelium of trachea	35	0.41	0.00	0.21	0.48	0.28	0.44	0.56	0.74
mesothelial cell	26	0.70	0.76	0.68	0.80	0.63	0.98	0.98	0.90
ciliated epithelial cell	31	0.95	0.00	0.56	0.62	0.44	0.98	0.97	0.97
mucus secreting cell	25	0.52	0.10	0.63	0.44	0.32	0.56	0.55	0.69
supporting cell of vestibular epithelium	30	0.91	0.00	0.68	0.74	0.40	0.97	0.92	0.98
enteroendocrine cell of small intestine	28	0.76	0.62	0.79	0.61	0.75	0.88	0.84	0.83
transit amplifying cell of colon	23	0.32	0.41	0.50	0.33	0.19	0.70	0.60	0.58
tracheal goblet cell	33	0.55	0.25	0.67	0.59	0.29	0.72	0.70	0.74
ovarian surface epithelial cell	15	0.00	0.11	0.32	0.69	0.71	0.97	0.90	0.90
glandular epithelial cell	7	0.86	0.09	0.22	0.27	0.48	0.93	0.88	1.00
paneth cell of colon	22	0.00	0.00	0.29	0.22	0.31	0.65	0.62	0.36
tuft cell of colon	18	0.00	0.23	0.65	0.40	0.47	0.95	0.82	0.69
ionocyte	18	0.86	0.73	0.43	0.80	0.40	0.88	0.79	0.95
neuro-medullary thymic epithelial cell	9	0.36	0.60	0.76	0.64	0.56	0.86	0.90	0.62
sebum secreting cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
type B pancreatic cell	9	0.70	0.00	0.82	0.71	0.55	0.89	0.80	0.89
myo-medullary thymic epithelial cell	10	0.76	0.00	0.00	0.90	0.46	1.00	0.95	1.00
interstitial cell of Cajal	5	0.53	0.00	1.00	0.67	0.19	0.91	1.00	1.00
peritubular myoid cell	12	0.00	0.00	0.50	0.59	0.53	1.00	0.96	0.67
retinal pigment epithelial cell	3	0.00	0.00	1.00	0.80	0.27	1.00	1.00	1.00
pancreatic A cell	4	0.00	0.00	0.89	0.40	0.44	1.00	1.00	1.00
vestibular dark cell	4	0.00	0.00	0.00	0.00	0.18	1.00	1.00	0.86
type L enteroendocrine cell	3	0.00	0.00	0.25	0.25	0.22	0.86	1.00	0.50
medullary thymic epithelial cell	3	0.00	0.00	0.00	0.00	0.00	0.86	0.57	0.00
transit amplifying cell of small intestine	7	0.00	0.00	0.25	0.00	0.07	0.44	0.20	0.25
taste receptor cell	2	0.00	0.00	0.00	0.00	0.36	0.00	0.40	0.67
enterochromaffin-like cell	4	0.00	0.00	0.00	0.29	0.73	1.00	0.86	0.67
pulmonary ionocyte	1	0.00	0.00	1.00	0.00	0.05	0.50	0.00	1.00
enteroendocrine cell	2	0.00	0.00	0.50	0.67	0.02	0.50	0.50	0.50
serous cell of epithelium of bronchus	2	0.00	0.00	0.00	0.67	0.67	0.00	0.67	0.67
pancreatic D cell	1	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
keratocyte	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
pancreatic PP cell	0	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
epithelial fate stem cell	0	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	scanvi	svm	xgboost	Consensus Prediction
basal cell	30114	0.87	0.81	0.91	0.84	0.85	0.86	0.86	0.94
bladder urothelial cell	24614	0.99	0.93	0.91	0.80	0.96	0.99	0.99	1.00
luminal epithelial cell of mammary gland	13885	0.99	0.27	0.97	0.80	0.97	0.98	0.98	1.00
enterocyte of epithelium proper of duodenum	12148	0.93	0.53	0.87	0.68	0.95	0.91	0.90	0.98
stratified squamous epithelial cell	11078	0.84	0.83	0.91	0.85	0.84	0.84	0.85	0.89
acinar cell of salivary gland	11026	0.96	0.89	0.93	0.81	0.95	0.97	0.96	0.98
pulmonary alveolar type 2 cell	10434	0.98	0.98	0.97	0.93	0.96	0.98	0.97	0.98
conjunctival epithelial cell	9995	0.93	0.72	0.84	0.70	0.95	0.96	0.95	0.97
luminal cell of prostate epithelium	9577	0.90	0.80	0.94	0.77	0.95	0.96	0.95	0.97
kidney epithelial cell	8341	0.99	0.85	0.95	0.76	0.98	1.00	1.00	1.00
hepatocyte	6674	1.00	1.00	0.97	0.82	0.99	1.00	1.00	1.00
enterocyte of epithelium proper of ileum	5784	0.98	0.13	0.86	0.57	0.98	0.98	0.98	0.99
pancreatic acinar cell	4937	0.97	0.76	0.96	0.81	0.98	0.98	0.98	0.98
enterocyte of epithelium of large intestine	4131	0.85	0.37	0.83	0.53	0.89	0.90	0.91	0.94
corneal epithelial cell	3766	0.92	0.00	0.94	0.86	0.93	0.96	0.95	0.96
duct epithelial cell	3502	0.82	0.64	0.87	0.72	0.84	0.88	0.84	0.92
basal cell of prostate epithelium	3167	0.73	0.03	0.92	0.72	0.89	0.87	0.85	0.91
pulmonary alveolar type 1 cell	2766	0.97	0.98	0.98	0.88	0.97	0.98	0.96	0.98
pancreatic ductal cell	2455	0.93	0.19	0.92	0.78	0.96	0.96	0.95	0.97
small intestine goblet cell	1856	0.91	0.86	0.93	0.72	0.90	0.95	0.93	0.96
BEST4+ enteroycte	1782	0.82	0.79	0.81	0.69	0.78	0.88	0.90	0.91
paneth cell of epithelium of small intestine	1668	0.69	0.61	0.76	0.50	0.69	0.72	0.73	0.85
club cell	1584	0.74	0.83	0.88	0.84	0.79	0.83	0.81	0.90
intestinal crypt stem cell of colon	1559	0.77	0.59	0.83	0.63	0.84	0.86	0.88	0.91
progenitor cell of mammary luminal epithelium	1522	0.98	0.00	0.98	0.96	0.88	0.86	0.91	0.99
epithelial cell	1474	0.95	0.87	0.79	0.64	0.98	0.98	0.97	0.98
large intestine goblet cell	1402	0.91	0.78	0.78	0.63	0.93	0.95	0.93	0.95
epithelial cell of uterus	1265	0.97	0.43	0.84	0.54	0.97	0.99	0.96	0.99
enterocyte of epithelium proper of small intestine	1264	0.43	0.00	0.70	0.42	0.75	0.75	0.78	0.89
acinar cell	1206	0.86	0.64	0.72	0.76	0.92	0.94	0.94	0.94
lung ciliated cell	1075	0.75	0.59	0.86	0.88	0.97	0.97	0.97	0.98
respiratory goblet cell	921	0.34	0.56	0.84	0.69	0.56	0.63	0.60	0.79
salivary gland cell	750	0.68	0.05	0.91	0.67	0.85	0.81	0.80	0.93
ciliated columnar cell of tracheobronchial tree	638	0.33	0.33	0.80	0.82	0.91	0.92	0.91	0.97
intrahepatic cholangiocyte	607	0.98	0.25	0.93	0.75	0.94	1.00	0.95	0.99
blood vessel smooth muscle cell	594	0.97	0.71	0.90	0.88	0.94	0.99	0.99	0.99
intestinal crypt stem cell of small intestine	533	0.13	0.29	0.33	0.15	0.56	0.61	0.68	0.70
myoepithelial cell	428	0.76	0.44	0.90	0.85	0.71	0.75	0.59	0.91
intestinal tuft cell	411	0.78	0.86	0.96	0.86	0.90	0.98	0.99	0.96
enterocyte of epithelium proper of jejunum	362	0.19	0.00	0.51	0.22	0.94	0.57	0.47	0.89
serous cell of epithelium of trachea	291	0.42	0.02	0.83	0.63	0.56	0.47	0.66	0.80
mesothelial cell	300	0.68	0.70	0.81	0.85	0.95	0.94	0.96	0.93
ciliated epithelial cell	289	0.91	0.01	0.62	0.71	0.93	1.00	0.98	0.99
mucus secreting cell	244	0.50	0.14	0.85	0.66	0.62	0.71	0.79	0.84
supporting cell of vestibular epithelium	237	0.89	0.00	0.60	0.76	0.95	1.00	0.95	0.99
enteroendocrine cell of small intestine	236	0.73	0.58	0.85	0.76	0.75	0.89	0.88	0.91
transit amplifying cell of colon	214	0.35	0.37	0.49	0.49	0.42	0.78	0.75	0.82
tracheal goblet cell	197	0.67	0.26	0.80	0.69	0.55	0.75	0.69	0.92
ovarian surface epithelial cell	213	0.00	0.13	0.79	0.78	0.97	0.99	0.97	0.97
glandular epithelial cell	210	0.88	0.19	0.59	0.64	0.86	0.95	0.93	0.98
paneth cell of colon	195	0.00	0.01	0.68	0.46	0.68	0.82	0.88	0.83
tuft cell of colon	160	0.00	0.36	0.89	0.54	0.80	0.93	0.96	0.94
ionocyte	142	0.65	0.63	0.71	0.70	0.59	0.87	0.81	0.89
neuro-medullary thymic epithelial cell	113	0.45	0.46	0.84	0.75	0.85	0.84	0.90	0.86
sebum secreting cell	105	0.74	0.02	0.86	0.57	0.74	0.95	0.86	0.98
type B pancreatic cell	93	0.70	0.00	0.91	0.80	0.58	1.00	0.99	0.99
myo-medullary thymic epithelial cell	67	0.60	0.00	0.87	0.82	0.66	0.99	0.98	0.99
interstitial cell of Cajal	65	0.51	0.00	1.00	0.78	0.53	0.98	0.98	1.00
peritubular myoid cell	55	0.00	0.00	0.49	0.53	0.73	1.00	0.96	0.87
retinal pigment epithelial cell	59	0.00	0.06	1.00	0.97	0.83	1.00	0.99	1.00
pancreatic A cell	44	0.00	0.00	0.89	0.84	0.84	1.00	0.99	1.00
vestibular dark cell	41	0.00	0.00	0.18	0.18	0.71	1.00	0.92	0.97
type L enteroendocrine cell	41	0.00	0.00	0.74	0.58	0.85	0.95	0.99	0.94
medullary thymic epithelial cell	31	0.00	0.00	0.41	0.23	0.76	0.85	0.86	0.98
transit amplifying cell of small intestine	27	0.00	0.00	0.29	0.00	0.14	0.84	0.87	0.90
taste receptor cell	30	0.00	0.08	0.29	0.48	0.48	0.83	0.34	0.97
enterochromaffin-like cell	23	0.00	0.00	0.81	0.51	0.75	1.00	1.00	0.95
pulmonary ionocyte	24	0.00	0.08	0.76	0.50	0.73	0.94	0.94	0.91
enteroendocrine cell	23	0.00	0.00	0.75	0.37	0.47	0.88	0.98	0.86
serous cell of epithelium of bronchus	13	0.00	0.14	0.00	0.70	0.43	1.00	1.00	0.96
pancreatic D cell	8	0.00	0.00	0.00	0.00	0.48	1.00	1.00	1.00
keratocyte	7	0.00	0.00	0.00	0.00	0.42	0.78	0.56	0.00
pancreatic PP cell	2	0.00	0.00	0.00	0.00	0.18	1.00	1.00	0.67
epithelial fate stem cell	2	0.00	0.00	0.00	0.00	0.05	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

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Collection including popV/tabula_sapiens_Epithelium

Tabula sapiens

Collection

Data underlying Tabula sapiens • 38 items • Updated Sep 26