polyICSFlow
This is the development version of polyICSFlow; to use it, please install the devel version of Bioconductor.
Identifying the Frequency of Polyfunctional Antigen-Specific T cells in ICS Flow Cytometry Data
Bioconductor version: Development (3.24)
polyICSFlow systematically identifies all cytokine combinations detected in an intracellular cytokine staining (ICS) flow cytometry assay and quantifies polyfunctional antigen-specific responses to single or multiple antigens. The package also offers versatile plotting options for efficient data exploration and visualization of cytokine co-expression profiles.
Author: Lisa Loksø Dietz [aut, cre] 
, Sofie Van Gassen [aut] , Sarah Bonte [aut] , Yvan Saeys [aut] , Ole Schmeltz Søgaard [aut]
Maintainer: Lisa Loksø Dietz <lisdie at clin.au.dk>
citation("polyICSFlow")):Lisa Loksø Dietz, Sofie Van Gassen, Sarah Bonte, Yvan Saeys, Ole Schmeltz Søgaard. polyICSFlow: Identifying the Frequency of Polyfunctional Antigen-Specific T cells in ICS Flow Cytometry Data. doi:10.18129/B9.bioc.polyICSFlow, R package version 0.99.6, https://bioconductor.org/packages/polyICSFlow.
Generated from the package metadata; it may differ from the package's own citation.
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("polyICSFlow")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("polyICSFlow")| getting_started | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FlowCytometry, Immunology, SingleCell, Software |
| Version | 0.99.6 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>=2) |
| Depends | R (>= 3.5.0) |
| Imports | flowCore, flowWorkspace, openCyto, FlowSOM, ComplexHeatmap, SummarizedExperiment, cowplot, dplyr, forcats, ggtext, rlang, scales, stringr, tidyselect, tidyr, magrittr, ggplot2, methods |
| System Requirements | |
| URL | https://github.com/SoegaardLab/polyICSFlow |
| Bug Reports | https://github.com/SoegaardLab/polyICSFlow/issues |
See More
| Suggests | knitr, rmarkdown, testthat (>= 3.0.0), patchwork, ggh4x |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | polyICSFlow_0.99.6.tar.gz |
| Windows Binary (x86_64) | polyICSFlow_0.99.6.zip |
| macOS Binary (big-sur-x86_64) | polyICSFlow_0.99.6.tgz |
| macOS Binary (sonoma-arm64) | polyICSFlow_0.99.6.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/polyICSFlow |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/polyICSFlow |
| Package Short Url | https://bioconductor.org/packages/polyICSFlow/ |
| Package Downloads Report | Download Stats |