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: Trachea'
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 |
|---|---|---|---|---|---|---|---|---|---|---|
| basal cell | 1041 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.96 | 0.98 | 0.97 | 0.99 |
| neutrophil | 451 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.97 | 0.98 | 0.99 | 0.99 |
| fibroblast | 171 | 0.97 | 0.96 | 0.97 | 0.96 | 0.00 | 0.96 | 0.97 | 0.97 | 0.98 |
| CD8-positive, alpha-beta T cell | 131 | 0.91 | 0.92 | 0.92 | 0.71 | 0.00 | 0.93 | 0.94 | 0.95 | 0.93 |
| ciliated columnar cell of tracheobronchial tree | 73 | 0.96 | 0.97 | 0.94 | 0.99 | 0.00 | 0.92 | 0.95 | 0.96 | 0.96 |
| macrophage | 63 | 0.97 | 0.97 | 0.93 | 0.95 | 0.00 | 0.94 | 0.96 | 0.95 | 0.97 |
| B cell | 66 | 0.98 | 0.98 | 0.99 | 0.66 | 0.00 | 0.99 | 0.98 | 0.99 | 0.99 |
| endothelial cell | 46 | 0.97 | 0.96 | 0.94 | 0.95 | 0.00 | 0.98 | 1.00 | 0.97 | 0.98 |
| serous cell of epithelium of trachea | 34 | 0.58 | 0.06 | 0.77 | 0.85 | 0.00 | 0.53 | 0.64 | 0.64 | 0.77 |
| plasma cell | 23 | 0.96 | 0.93 | 0.93 | 0.87 | 0.00 | 0.93 | 0.96 | 0.91 | 0.96 |
| CD4-positive, alpha-beta T cell | 31 | 0.81 | 0.79 | 0.79 | 0.05 | 0.00 | 0.82 | 0.85 | 0.88 | 0.86 |
| mucus secreting cell | 31 | 0.77 | 0.81 | 0.86 | 0.86 | 0.00 | 0.76 | 0.78 | 0.79 | 0.86 |
| tracheal goblet cell | 33 | 0.78 | 0.67 | 0.86 | 0.88 | 0.00 | 0.82 | 0.89 | 0.89 | 0.94 |
| connective tissue cell | 9 | 0.84 | 0.00 | 0.95 | 0.75 | 0.00 | 0.86 | 0.86 | 0.90 | 1.00 |
| smooth muscle cell | 15 | 0.82 | 0.90 | 0.82 | 0.79 | 0.00 | 0.80 | 0.82 | 0.85 | 0.82 |
| mast cell | 16 | 0.97 | 0.97 | 1.00 | 1.00 | 0.00 | 1.00 | 0.97 | 0.97 | 1.00 |
| monocyte | 5 | 0.80 | 0.67 | 0.67 | 0.00 | 0.00 | 0.73 | 1.00 | 0.80 | 0.89 |
| natural killer cell | 9 | 0.64 | 0.75 | 0.75 | 0.18 | 0.00 | 0.64 | 0.76 | 0.73 | 0.80 |
| granulocyte | 6 | 0.00 | 0.00 | 0.29 | 0.00 | 0.00 | 0.26 | 0.50 | 0.44 | 0.00 |
| mature NK T cell | 5 | 0.25 | 0.00 | 0.50 | 0.33 | 0.00 | 0.57 | 0.73 | 0.80 | 0.25 |
| T cell | 2 | 0.00 | 0.67 | 0.67 | 0.00 | 0.00 | 0.33 | 0.00 | 0.00 | 0.00 |
| ionocyte | 2 | 0.50 | 0.00 | 0.50 | 0.67 | 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 | 0.00 | 0.00 |
| intermediate monocyte | 1 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| non-classical monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| innate lymphoid cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
| plasmacytoid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| basal cell | 9206 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |
| neutrophil | 4233 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |
| fibroblast | 1629 | 0.96 | 0.92 | 0.98 | 0.98 | 0.00 | 0.96 | 0.99 | 0.99 | 0.98 |
| CD8-positive, alpha-beta T cell | 1071 | 0.91 | 0.90 | 0.94 | 0.83 | 0.00 | 0.96 | 0.98 | 0.98 | 0.96 |
| ciliated columnar cell of tracheobronchial tree | 640 | 0.97 | 0.96 | 0.96 | 0.99 | 0.00 | 0.93 | 0.98 | 0.97 | 0.99 |
| macrophage | 649 | 0.92 | 0.92 | 0.95 | 0.93 | 0.00 | 0.95 | 0.98 | 0.99 | 0.97 |
| B cell | 561 | 0.97 | 0.95 | 0.98 | 0.81 | 0.00 | 0.99 | 1.00 | 1.00 | 0.99 |
| endothelial cell | 540 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 0.99 |
| serous cell of epithelium of trachea | 292 | 0.63 | 0.03 | 0.89 | 0.89 | 0.00 | 0.67 | 0.76 | 0.79 | 0.88 |
| plasma cell | 269 | 0.97 | 0.97 | 0.99 | 0.95 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |
| CD4-positive, alpha-beta T cell | 247 | 0.73 | 0.61 | 0.78 | 0.34 | 0.00 | 0.86 | 0.94 | 0.95 | 0.86 |
| mucus secreting cell | 239 | 0.75 | 0.73 | 0.89 | 0.89 | 0.00 | 0.84 | 0.87 | 0.86 | 0.92 |
| tracheal goblet cell | 199 | 0.69 | 0.51 | 0.89 | 0.88 | 0.00 | 0.83 | 0.88 | 0.86 | 0.93 |
| connective tissue cell | 143 | 0.78 | 0.00 | 0.93 | 0.92 | 0.00 | 0.92 | 0.96 | 0.92 | 0.96 |
| smooth muscle cell | 116 | 0.80 | 0.73 | 0.87 | 0.89 | 0.00 | 0.80 | 0.91 | 0.91 | 0.87 |
| mast cell | 103 | 0.96 | 0.96 | 0.96 | 0.97 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |
| monocyte | 76 | 0.52 | 0.52 | 0.71 | 0.63 | 0.00 | 0.88 | 0.96 | 0.97 | 0.85 |
| natural killer cell | 55 | 0.63 | 0.61 | 0.77 | 0.42 | 0.00 | 0.85 | 0.92 | 0.92 | 0.94 |
| granulocyte | 33 | 0.00 | 0.00 | 0.10 | 0.11 | 0.00 | 0.22 | 0.56 | 0.62 | 0.21 |
| mature NK T cell | 32 | 0.28 | 0.00 | 0.69 | 0.33 | 0.00 | 0.87 | 0.97 | 0.97 | 0.87 |
| T cell | 17 | 0.00 | 0.00 | 0.64 | 0.00 | 0.00 | 0.74 | 1.00 | 0.97 | 0.90 |
| ionocyte | 16 | 0.47 | 0.00 | 0.81 | 0.64 | 0.00 | 0.85 | 0.97 | 1.00 | 0.97 |
| regulatory T cell | 14 | 0.00 | 0.12 | 0.32 | 0.24 | 0.00 | 0.79 | 1.00 | 1.00 | 0.78 |
| intermediate monocyte | 15 | 0.00 | 0.00 | 0.50 | 0.29 | 0.00 | 0.79 | 1.00 | 1.00 | 0.80 |
| non-classical monocyte | 4 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.47 | 1.00 | 1.00 | 0.67 |
| innate lymphoid cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.36 | 0.80 | 0.80 | 1.00 |
| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |
| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.25 | 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