Cellpypes is an R package that uses the popular piping operator %>% to manually annotate cell types in single-cell RNA sequencing data. It can be applied to UMI data (e.g. 10x Genomics). Find cell type rules (gene+threshold) through exploration, use the `rule` command to reconstruct complex cell type hierarchies, then obtain cell type labels or pseudobulks. cellpypes models technical noise to find positive and negative cells for a given expression threshold, computes within seconds even on hundred-thousands of cells and thus unlocks scalable and reproducible manual annotation for single-cell data.

Visit the webpage https://github.com/FelixTheStudent/cellpypes.