Package: polyICSFlow 0.99.3

Lisa Loksø Dietz

polyICSFlow: Identifying the Frequency of Polyfunctional Antigen-Specific T cells in ICS Flow Cytometry Data

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.

Authors:Lisa Loksø Dietz [aut, cre], Sofie Van Gassen [aut], Sarah Bonte [aut], Yvan Saeys [aut], Ole Schmeltz Søgaard [aut]

polyICSFlow_0.99.3.tar.gz
polyICSFlow_0.99.3.zip(r-4.7)polyICSFlow_0.99.3.zip(r-4.6)polyICSFlow_0.99.3.zip(r-4.5)
polyICSFlow_0.99.3.tgz(r-4.6-any)polyICSFlow_0.99.3.tgz(r-4.5-any)
polyICSFlow_0.99.3.tar.gz(r-4.7-any)polyICSFlow_0.99.3.tar.gz(r-4.6-any)
polyICSFlow_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
polyICSFlow/json (API)
NEWS

# Install 'polyICSFlow' in R:

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

Bug tracker:https://github.com/soegaardlab/polyicsflow/issues

On CRAN:

flowcytometry immunology software singlecell

3.30 score 9 exports 152 dependencies

Last updated from:036ed01f86. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	220
linux-devel-x86_64	OK	345
source / vignettes	OK	516
linux-release-x86_64	OK	400
macos-release-arm64	OK	256
macos-oldrel-arm64	OK	274
windows-devel	OK	375
windows-release	OK	350
windows-oldrel	OK	317
wasm-release	OK	164

Exports:%>%assignMarkerCombinations calcPolyfunctionality extractCellCounts getMarkerPositivity plotCellCountsAtLeast plotCellCountsExactly plotMarkerComb2DScatters plotMarkerCombHeatmap

Dependencies:abind ALL backports base64enc BH Biobase BiocGenerics biocmake boot broom car carData circlize cli clue cluster codetools colorRamps colorspace commonmark ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon curl cytolib data.table DelayedArray deldir Deriv digest dir.expiry doBy doParallel dplyr farver filelock flowClust flowCore FlowSOM flowViz flowWorkspace forcats foreach forecast Formula fracdiff generics GenomicRanges GetoptLong ggforce ggnewscale ggplot2 ggpubr ggrepel ggsci ggsignif ggtext GlobalOptions glue graph gridExtra gridtext gtable hexbin IDPmisc igraph interp IRanges isoband iterators jpeg jsonlite KernSmooth labeling lattice latticeExtra lifecycle litedown lme4 lmtest magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv microbenchmark minqa modelr ncdfFlow nlme nloptr nnet numDeriv openCyto pbkrtest pillar pkgconfig png polyclip polynom purrr quantreg R6 RBGL rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas Rgraphviz Rhdf5lib rjson rlang RProtoBufLib rstatix Rtsne S4Arrays S4Vectors S7 scales Seqinfo shape SparseArray SparseM stringi stringr SummarizedExperiment survival systemfonts tibble tidyr tidyselect timeDate tweenr urca utf8 vctrs viridisLite withr xfun XML xml2 XVector zoo

PolyICSFlow: Identifying the Frequency of Polyfunctional Antigen-Specific T cells in ICS Flow Cytometry Data

Rendered fromgetting_started.Rmdusingknitr::rmarkdownon Jun 11 2026.

Last update: 2026-06-11
Started: 2026-04-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assing each cell to a combination of gated markers.	assignMarkerCombinations
Calculate the frequency of polyfunctional cells	calcPolyfunctionality
Get number of cells positive for each distinct marker combination	extractCellCounts
Create dataframe of marker positivity	getMarkerPositivity
Plot counts of cells expressing at least 1, 2, ..., n markers.	plotCellCountsAtLeast
Plot counts of cells expressing exactly 1, 2, ..., n markers.	plotCellCountsExactly
Plot 2D scatterplots of all marker combinations.	plotMarkerComb2DScatters
Plot a heatmap of all possible marker combinations.	plotMarkerCombHeatmap