Annotate single-cell RNA sequencing data manually based on marker gene thresholds. Find cell type rules (gene+threshold) through exploration, use the popular piping operator '%>%' to reconstruct complex cell type hierarchies. 'cellpypes' models technical noise to find positive and negative cells for a given expression threshold and returns cell type labels or pseudobulks. Cite this package as Frauhammer (2022) <doi:10.5281/zenodo.6555728> and visit <https://github.com/FelixTheStudent/cellpypes> for tutorials and newest features.
Version: 0.3.0 Depends: R (≥ 2.10) Imports: scUtils, ggplot2, Matrix, rlang, viridis, cowplot, dplyr, scales, methods, scattermore Suggests: testthat (≥ 3.0.0), knitr, rmarkdown, Seurat, DESeq2, RcppAnnoy, tibble, SeuratObject Published: 2024-01-27 DOI: 10.32614/CRAN.package.cellpypes Author: Felix Frauhammer [aut, cre] Maintainer: Felix Frauhammer <felixfrauhammer at gmail.com> BugReports: https://github.com/FelixTheStudent/cellpypes/issues License: GPL (≥ 3) URL: https://github.com/FelixTheStudent/cellpypes NeedsCompilation: no Citation: cellpypes citation info Materials: README NEWS CRAN checks: cellpypes results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=cellpypes to link to this page.
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