CySA
This is the development version of CySA; to use it, please install the devel version of Bioconductor.
Interactive Cluster Selector for Cytometry Data
Bioconductor version: 3.24 · Package version: 0.99.28
CySA provides an interactive Shiny-based tool for analyzing flow and mass cytometry data. It supports self-organizing map (SOM) based clustering, dimension reduction (t-SNE, UMAP, PCA), and statistical comparison of cell populations across sample groups. Users can select cell clusters interactively via 2D scatter plots, dendrograms, or SOM node grids, and explore marker expression patterns across the selected populations.
Author: Bernd Jagla [aut, cre] 
Maintainer: Bernd Jagla <bernd.jagla at pasteur.fr>
Citation
From within R, enter citation("CySA"):
Bernd Jagla. CySA: Interactive Cluster Selector for Cytometry Data. doi:10.18129/B9.bioc.CySA, R package version 0.99.28, https://bioconductor.org/packages/CySA.
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("CySA")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 0.99.28 |
| License | MIT + file LICENSE |
| URL | https://github.com/baj12/CySA |
| Bug Reports | https://github.com/baj12/CySA/issues |
| Last updated | 2026-08-02 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| Downloads rank | 2430 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Clustering, FlowCytometry, ShinyApps, SingleCell, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/CySA/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CySA")| Introduction to CySA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | CySA_0.99.28.tar.gz |
| Windows binary (x86_64) | CySA_0.99.28.zip |
| macOS binary (arm64) | CySA_0.99.28.tgz |
| macOS binary (x86_64) | CySA_0.99.28.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CySA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CySA |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0)
Imports: shiny, shinydashboard, shinydashboardPlus, shinyjs, shinyjqui, htmltools, SingleCellExperiment, S4Vectors, SummarizedExperiment, Matrix, tidyselect, matrixStats, RColorBrewer, CATALYST, FlowSOM, dplyr, tidyr, tibble, data.table, stringr, purrr, reshape2, rlang, raster, ggplot2, plotly, viridis, dendextend, ComplexHeatmap, cowplot, Rtsne, umap, DT, collapsibleTree, withr
Suggests: KernSmooth, knitr, jsonlite, rmarkdown, shinytest2, testthat (>= 3.0.0)