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")):
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("polyICSFlow")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | FlowCytometry, Immunology, SingleCell, Software |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | GPL (>=2) |
| Depends | |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |