Hugging Face's logo

popV
/
tabula_sapiens_Prostate

Joblib
popV
biology
genomics
single-cell
anndata_version:0.11.3
python_version:3.11.11
tissue: Prostate
Model card Files Community
tabula_sapiens_Prostate / README.md
canergen's picture
canergen
Upload README.md with huggingface_hub
002c6fd verified
preview code
|
raw
history blame
4.65 kB
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: Prostate'

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
luminal cell of prostate epithelium 1052 0.94 0.97 0.97 0.94 0.00 0.94 0.95 0.93 0.96
basal cell of prostate epithelium 352 0.85 0.89 0.90 0.84 0.00 0.87 0.87 0.84 0.90
CD8-positive, alpha-beta T cell 256 0.94 0.88 0.95 0.88 0.00 0.93 0.92 0.93 0.96
endothelial cell 121 0.98 0.97 0.97 0.94 0.00 0.97 0.97 0.97 0.98
macrophage 94 0.96 0.98 0.98 0.96 0.00 0.99 0.97 0.97 0.98
fibroblast 59 0.96 0.95 0.97 0.84 0.00 0.94 0.95 0.94 0.97
mature NK T cell 51 0.93 0.15 0.91 0.32 0.00 0.93 0.94 0.91 0.96
smooth muscle cell 48 0.92 0.95 0.91 0.80 0.00 0.92 0.92 0.91 0.96
neutrophil 23 0.98 0.98 0.98 0.89 0.00 0.96 0.96 1.00 0.98
erythrocyte 21 0.85 0.91 0.95 0.95 0.00 0.83 0.98 0.93 0.98
CD4-positive, alpha-beta T cell 13 0.11 0.00 0.25 0.00 0.00 0.44 0.39 0.53 0.24
B cell 8 0.75 0.86 0.80 0.75 0.00 0.89 0.93 0.86 0.80
mast cell 4 1.00 0.75 1.00 0.67 0.00 0.35 0.89 1.00 1.00
T cell 1 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
luminal cell of prostate epithelium 9600 0.94 0.96 0.98 0.97 0.00 0.94 0.95 0.94 0.96
basal cell of prostate epithelium 3143 0.85 0.87 0.94 0.91 0.00 0.87 0.89 0.86 0.90
CD8-positive, alpha-beta T cell 2260 0.95 0.88 0.96 0.91 0.00 0.92 0.95 0.95 0.97
endothelial cell 1084 0.98 0.92 0.98 0.96 0.00 0.97 0.98 0.97 0.99
macrophage 928 0.98 0.98 0.98 0.98 0.00 0.99 0.99 0.99 0.99
fibroblast 460 0.96 0.95 0.98 0.86 0.00 0.96 0.98 0.98 0.99
mature NK T cell 436 0.91 0.18 0.92 0.54 0.00 0.92 0.92 0.93 0.95
smooth muscle cell 429 0.93 0.91 0.97 0.83 0.00 0.94 0.97 0.97 0.99
neutrophil 238 0.99 0.98 0.99 0.95 0.00 0.99 1.00 1.00 1.00
erythrocyte 118 0.87 0.86 0.97 0.93 0.00 0.83 0.99 0.99 0.98
CD4-positive, alpha-beta T cell 103 0.26 0.00 0.23 0.09 0.00 0.47 0.67 0.69 0.43
B cell 93 0.82 0.82 0.84 0.90 0.00 0.92 0.99 0.98 0.97
mast cell 22 1.00 0.64 0.98 0.68 0.00 0.38 0.98 0.98 1.00
T cell 13 0.00 0.00 0.25 0.00 0.00 0.75 0.96 0.67 0.83

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