SuperCellCyto

This is the released version of SuperCellCyto; for the devel version, see SuperCellCyto.

SuperCell For Cytometry Data

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DOI: 10.18129/B9.bioc.SuperCellCyto

Bioconductor version: Release (3.22)

SuperCellCyto provides the ability to summarise cytometry data into supercells by merging together cells that are similar in their marker expressions using the SuperCell package.

Author: Givanna Putri [aut, cre] ORCID iD ORCID: 0000-0002-7399-8014 , George Howitt [aut], Felix Marsh-Wakefield [aut], Thomas Ashhurst [aut], Belinda Phipson [aut]

Maintainer: Givanna Putri <givanna.h at gmail.com>

Citation (from within R, enter citation("SuperCellCyto")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("SuperCellCyto")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SuperCellCyto")

How to create supercells HTML R Script

how_to_prepare_data HTML R Script

interoperability_with_seurat HTML R Script

Using SuperCellCyto with Single-Cell Based Objects HTML R Script

using-runsupercellcyto-for-stratified-summarising HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CellBiology, FlowCytometry, SingleCell, Software

Version 1.0.0

In Bioconductor since BioC 3.22 (R-4.5) (< 6 months)

License GPL-3 + file LICENSE

Depends

Imports SuperCell, data.table, Matrix, BiocParallel

System Requirements

URL https://phipsonlab.github.io/SuperCellCyto/

Bug Reports https://github.com/phipsonlab/SuperCellCyto/issues

Suggests flowCore, knitr, rmarkdown, usethis, testthat (>= 3.0.0), BiocSingular, bluster, scater, scran, Seurat, SingleCellExperiment, BiocStyle, magick, qs2

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SuperCellCyto_1.0.0.tar.gz

Windows Binary (x86_64) SuperCellCyto_1.0.0.zip

macOS Binary (x86_64) SuperCellCyto_1.0.0.tgz

macOS Binary (arm64) SuperCellCyto_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/SuperCellCyto

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SuperCellCyto

Bioc Package Browser https://code.bioconductor.org/browse/SuperCellCyto/

Package Short Url https://bioconductor.org/packages/SuperCellCyto/

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