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 |
Documentation:
Downloads:
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