Package: CySA 0.99.28

Bernd Jagla

CySA: Interactive Cluster Selector for Cytometry Data

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.

Authors:Bernd Jagla [aut, cre]

CySA_0.99.28.tar.gz
CySA_0.99.28.zip(r-4.7-any)CySA_0.99.28.zip(r-4.6-any)CySA_0.99.28.zip(r-4.5-any)
CySA_0.99.28.tgz(r-4.6-any)CySA_0.99.28.tgz(r-4.5-any)
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CySA_0.99.28.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CySA/json (API)

# Install 'CySA' in R:

install.packages('CySA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/baj12/cysa/issues

On BioConductor:CySA-0.99.28(bioc 3.24)

singlecell flowcytometry clustering visualization shinyapps

4.30 score 1 stars 234 downloads 7 exports 222 dependencies

Last updated from:fab459b702. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	434
linux-devel	OK	1135
source / vignettes	OK	504
linux-release	OK	1064
macos-release	OK	658
macos-oldrel	OK	810
windows-devel	OK	835
windows-release	OK	1260
windows-oldrel	OK	1019
wasm-release	OK	389

Exports:clusterSelector CySA_default_cluster_cols CySA_example_sce plotCytoScatter plotSOMScatter prepClusterSelector prepClusterSelectorData

Dependencies:abind ALL askpass assorthead backports base64enc beachmat beeswarm BH Biobase BiocGenerics biocmake BiocNeighbors BiocParallel BiocSingular boot broom bslib cachem car carData CATALYST circlize cli clue cluster codetools collapsibleTree colorRamps colorspace commonmark ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon crosstalk curl cytolib data.table data.tree DelayedArray dendextend Deriv digest dir.expiry doBy doParallel dplyr dqrng drc DT evaluate farver fastmap filelock flowCore FlowSOM FNN fontawesome foreach forecast formatR Formula fracdiff fresh fs futile.logger futile.options generics GenomicRanges GetoptLong ggbeeswarm ggforce ggnewscale ggplot2 ggpubr ggrepel ggridges ggsci ggsignif GlobalOptions glue gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr igraph IRanges irlba isoband iterators jquerylib jsonlite knitr labeling lambda.r later lattice lazyeval lifecycle lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa modelr multcomp mvtnorm nlme nloptr nnet nnls numDeriv openssl otel pbkrtest pheatmap pillar pkgconfig plotly plotrix plyr png polyclip polynom promises purrr quantreg R6 rappdirs raster rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress RcppTOML Rdpack reformulas reshape2 reticulate Rhdf5lib rjson rlang rmarkdown rprojroot RProtoBufLib RSpectra rstatix rstudioapi rsvd Rtsne S4Arrays S4Vectors S7 sandwich sass ScaledMatrix scales scater scuttle Seqinfo shape shiny shinydashboard shinydashboardPlus shinyjqui shinyjs SingleCellExperiment sitmo snow sourcetools sp SparseArray SparseM stringi stringr SummarizedExperiment survival sys systemfonts terra TH.data tibble tidyr tidyselect timeDate tinytex tweenr umap urca utf8 uwot vctrs vipor viridis viridisLite waiter withr xfun XML xtable XVector yaml zoo

Introduction to CySA

Rendered fromintro.Rmdusingknitr::rmarkdown

Last update: 2026-08-02
Started: 2026-06-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cluster Selector Shiny Application	clusterSelector
Default cluster color palette	CySA_default_cluster_cols
Minimal example SingleCellExperiment for CySA	CySA_example_sce
Plot Scatter for a SingleCellExperiment	plotCytoScatter
Scatter plot	plotSOMScatter
Prepare Cluster Selector Outputs	prepClusterSelector
Prepare Data for the Cluster Selector Shiny App	prepClusterSelectorData