scTypeEval Documentation
Evaluate Cell Type Annotation Consistency in Single-Cell Data
scTypeEval is an R/Bioconductor package to evaluate cell type annotation quality in single-cell transcriptomics when ground truth labels are unavailable. It provides internal consistency metrics to benchmark manual annotations, automated label transfer, or clustering-derived labels across samples and datasets.
Main package resources
- GitHub repository: https://github.com/carmonalab/scTypeEval
- Bioconductor package: https://www.bioconductor.org/packages/release/bioc/html/scTypeEval.html
- Issues and comments: https://github.com/carmonalab/scTypeEval/issues
Documentation in this site
Citation
If you use scTypeEval, please cite:
Garnica J, Andreatta M, Carmona SJ (2026). Evaluating cell type annotations in single-cell omics in the absence of ground truth. bioRxiv. https://doi.org/10.64898/2026.06.10.731285
For citation details, see Citation.