SuperCellCyto
This is the development version of SuperCellCyto; for the stable release version, see SuperCellCyto.
SuperCell For Cytometry Data
Bioconductor version: Development (3.24)
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]
, George Howitt [aut], Felix Marsh-Wakefield [aut], Thomas Ashhurst [aut], Belinda Phipson [aut]
Maintainer: Givanna Putri <givanna.h at gmail.com>
citation("SuperCellCyto")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CellBiology, FlowCytometry, SingleCell, Software |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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 |
See More
| Suggests | flowCore, knitr, rmarkdown, usethis, testthat (>= 3.0.0), BiocSingular, bluster, scater, scran, Seurat, SingleCellExperiment, BiocStyle, magick, qs2 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SuperCellCyto_1.3.0.tar.gz |
| Windows Binary (x86_64) | SuperCellCyto_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | SuperCellCyto_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | SuperCellCyto_1.3.0.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/ |
| Package Downloads Report | Download Stats |