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popV
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tabula_sapiens_Bladder

Joblib
popV
biology
genomics
single-cell
anndata_version:0.11.3
python_version:3.11.11
tissue: Bladder
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metadata
library_name: popV
license: cc-by-4.0
tags:
  - biology
  - genomics
  - single-cell
  - anndata_version:0.11.3
  - python_version:3.11.11
  - popV
  - 'tissue: Bladder'

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
bladder urothelial cell 2798 0.99 0.99 0.99 0.99 0.00 0.96 0.99 0.98 0.99
fibroblast 1333 0.96 0.96 0.98 0.97 0.00 0.93 0.95 0.95 0.97
monocyte 471 0.86 0.91 0.91 0.90 0.00 0.88 0.86 0.88 0.91
CD8-positive, alpha-beta T cell 402 0.86 0.88 0.88 0.73 0.00 0.87 0.85 0.91 0.91
macrophage 344 0.84 0.89 0.89 0.89 0.00 0.84 0.85 0.87 0.89
myofibroblast cell 306 0.88 0.92 0.94 0.92 0.00 0.84 0.88 0.87 0.91
CD4-positive, alpha-beta T cell 234 0.71 0.77 0.74 0.52 0.00 0.75 0.79 0.86 0.84
mast cell 165 0.98 0.99 0.99 0.99 0.00 0.98 0.98 0.98 0.99
plasma cell 137 0.95 0.97 0.99 0.97 0.00 0.96 0.97 0.97 0.98
pericyte 100 0.95 0.95 0.94 0.95 0.00 0.91 0.92 0.94 0.94
smooth muscle cell 102 0.96 0.98 0.98 0.96 0.00 0.96 0.96 0.94 0.98
T cell 70 0.32 0.10 0.44 0.18 0.00 0.47 0.50 0.58 0.58
B cell 49 0.96 0.94 0.93 0.94 0.00 0.94 0.91 0.89 0.94
vein endothelial cell 42 0.80 0.83 0.79 0.70 0.00 0.84 0.81 0.84 0.83
neutrophil 21 0.79 0.95 0.95 0.81 0.00 0.40 0.87 0.87 0.87
natural killer cell 16 0.59 0.29 0.77 0.31 0.00 0.53 0.65 0.71 0.73
endothelial cell of lymphatic vessel 12 0.85 0.87 0.77 0.22 0.00 0.80 0.85 0.80 0.85
capillary endothelial cell 9 0.46 0.47 0.60 0.50 0.00 0.33 0.59 0.71 0.53
erythrocyte 9 0.64 0.31 1.00 0.62 0.00 0.20 0.95 0.58 0.95
mature NK T cell 10 0.57 0.18 0.62 0.33 0.00 0.67 0.86 0.76 0.89
endothelial cell 7 0.00 0.00 0.00 0.44 0.00 0.29 0.60 0.36 0.44
regulatory T cell 2 0.00 0.00 0.00 0.00 0.00 0.03 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
bladder urothelial cell 24443 0.99 0.99 0.99 0.99 0.00 0.96 0.99 0.99 0.99
fibroblast 12433 0.96 0.96 0.98 0.97 0.00 0.93 0.95 0.95 0.97
monocyte 4384 0.89 0.91 0.95 0.94 0.00 0.90 0.91 0.91 0.94
CD8-positive, alpha-beta T cell 4030 0.87 0.88 0.92 0.80 0.00 0.87 0.88 0.91 0.92
macrophage 2808 0.83 0.87 0.93 0.92 0.00 0.85 0.87 0.88 0.92
myofibroblast cell 2830 0.86 0.90 0.94 0.93 0.00 0.84 0.88 0.87 0.92
CD4-positive, alpha-beta T cell 1955 0.70 0.70 0.80 0.62 0.00 0.74 0.83 0.89 0.86
mast cell 1403 0.97 0.98 0.99 0.99 0.00 0.98 0.99 0.97 0.99
plasma cell 1068 0.96 0.96 0.98 0.99 0.00 0.97 0.99 0.98 0.99
pericyte 1084 0.96 0.96 0.97 0.96 0.00 0.95 0.97 0.97 0.98
smooth muscle cell 951 0.95 0.96 0.97 0.97 0.00 0.96 0.96 0.95 0.97
T cell 711 0.48 0.11 0.56 0.29 0.00 0.56 0.63 0.67 0.72
B cell 435 0.94 0.94 0.96 0.96 0.00 0.94 0.95 0.96 0.97
vein endothelial cell 396 0.83 0.86 0.90 0.85 0.00 0.94 0.96 0.97 0.95
neutrophil 220 0.85 0.96 0.98 0.90 0.00 0.48 0.97 0.91 0.96
natural killer cell 149 0.59 0.26 0.71 0.50 0.00 0.66 0.76 0.75 0.78
endothelial cell of lymphatic vessel 115 0.90 0.91 0.93 0.61 0.00 0.97 0.98 0.99 0.97
capillary endothelial cell 98 0.35 0.48 0.72 0.71 0.00 0.87 0.98 0.98 0.90
erythrocyte 97 0.70 0.33 0.97 0.81 0.00 0.23 0.94 0.68 0.94
mature NK T cell 85 0.52 0.33 0.72 0.43 0.00 0.79 0.87 0.91 0.91
endothelial cell 30 0.00 0.00 0.40 0.49 0.00 0.54 0.98 0.94 0.87
regulatory T cell 21 0.00 0.00 0.09 0.00 0.00 0.09 0.95 0.89 0.55

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