cellpypes: Cell Type Pipes for Single-Cell RNA Sequencing Data

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


Reference manual: cellpypes.pdf


Package source: cellpypes_0.3.0.tar.gz
Windows binaries: r-devel: cellpypes_0.3.0.zip, r-release: cellpypes_0.3.0.zip, r-oldrel: cellpypes_0.3.0.zip
macOS binaries: r-release (arm64): cellpypes_0.3.0.tgz, r-oldrel (arm64): cellpypes_0.3.0.tgz, r-release (x86_64): cellpypes_0.3.0.tgz, r-oldrel (x86_64): cellpypes_0.3.0.tgz
Old sources: cellpypes archive


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