Package: cellpypes 0.2.1

Felix Frauhammer

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.

Authors:Felix Frauhammer [aut, cre]

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cellpypes.pdf |cellpypes.html✨
cellpypes/json (API)
NEWS

Peer review:

Bug tracker:https://github.com/felixthestudent/cellpypes/issues

On CRAN:

celltype-annotationclassification-algorithmscrnaseqsingle-cell-rna-seq

12 exports 51 stars 3.12 score 37 dependencies 7 scripts 230 downloads

Last updated 8 months agofrom:1b8c15d910. Checks:OK: 7. Indexed: yes.

Exports:class_to_deseq2classifyfeatfind_knnplot_classesplot_lastpool_across_neighborspseudobulkpseudobulk_idpype_code_templatepype_from_seuratrule

Dependencies:assertthatclicolorspacecowplotdplyrfansifarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalesscattermorescUtilstibbletidyselectutf8vctrsviridisviridisLitewithr