Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2019) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2020) <arXiv:2005.07946> (open access),
Raymaekers and Rousseeuw (2020) <arXiv:1912.12446> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples" and "DI_examples".

Tools for detecting cellwise outliers and robust methods to analyze
data which may contain them. Contains the implementation of the algorithms described in
Rousseeuw and Van den Bossche (2018) <doi:10.1080/00401706.2017.1340909> (open access)
Hubert et al. (2019) <doi:10.1080/00401706.2018.1562989> (open access),
Raymaekers and Rousseeuw (2019) <doi:10.1080/00401706.2019.1677270> (open access),
Raymaekers and Rousseeuw (2020) <doi:10.1007/s10994-021-05960-5> (open access),
Raymaekers and Rousseeuw (2020) <doi:10.52933/jdssv.v1i3.18> (open access).
Examples can be found in the vignettes:
"DDC_examples", "MacroPCA_examples", "wrap_examples", "transfo_examples", "DI_examples" and "cellMCD_examples".

Cell Type Pipes for Single-Cell RNA Sequencing Data
person(given = "Felix",
family = "Frauhammer",
role = c("aut", "cre"),
email = "felixfrauhammer@gmail.com")
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.
testthat (>= 3.0.0), knitr, rmarkdown, Seurat, DESeq2,
RcppAnnoy, tibble, SeuratObject
scUtils, ggplot2, Matrix, rlang, viridis, cowplot, dplyr,
scales, methods, scattermore