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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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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.