# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 28 April 2026

#### Abstract

This vignette provides links to videos demonstrating some of the functionalities of CytoPipeline R package suite. It is distributed, as well as the accompanying videos, under a CC BY-SA license.

#### Package

CytoPipeline 1.12.0

# 1 Introduction

# 2 Background information

# 3 Illustrating dataset

# 4 Specifying the pipeline

# 5 Running the pipeline

# 6 Visualizing the results

# 7 Comparing pipelines

# 8 Example with two different QC methods

# 9 Visualizing scale transformations

# 10 Defining technical run parameters

# Session information

    ## R version 4.6.0 Patched (2026-04-24 r89963)
    ## Platform: aarch64-apple-darwin23
    ## Running under: macOS Tahoe 26.3.1
    ##
    ## Matrix products: default
    ## BLAS:   /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
    ##
    ## locale:
    ## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    ##
    ## time zone: America/New_York
    ## tzcode source: internal
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] ggplot2_4.0.3       reshape2_1.4.5      CytoPipeline_1.12.0
    ## [4] BiocStyle_2.40.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] changepoint_2.3       tidyselect_1.2.1      dplyr_1.2.1
    ##  [4] farver_2.1.2          blob_1.3.0            filelock_1.0.3
    ##  [7] S7_0.2.2              fastmap_1.2.0         BiocFileCache_3.2.0
    ## [10] XML_3.99-0.23         digest_0.6.39         lifecycle_1.0.5
    ## [13] cluster_2.1.8.2       RSQLite_2.4.6         magrittr_2.0.5
    ## [16] compiler_4.6.0        rlang_1.2.0           sass_0.4.10
    ## [19] tools_4.6.0           yaml_2.3.12           data.table_1.18.2.1
    ## [22] knitr_1.51            labeling_0.4.3        bit_4.6.0
    ## [25] curl_7.1.0            diagram_1.6.5         plyr_1.8.9
    ## [28] RColorBrewer_1.1-3    withr_3.0.2           purrr_1.2.2
    ## [31] RProtoBufLib_2.24.0   BiocGenerics_0.58.0   PeacoQC_1.22.0
    ## [34] grid_4.6.0            stats4_4.6.0          flowAI_1.42.0
    ## [37] colorspace_2.1-2      scales_1.4.0          iterators_1.0.14
    ## [40] tinytex_0.59          dichromat_2.0-0.1     cli_3.6.6
    ## [43] rmarkdown_2.31        crayon_1.5.3          ncdfFlow_2.58.0
    ## [46] generics_0.1.4        otel_0.2.0            rjson_0.2.23
    ## [49] DBI_1.3.0             cachem_1.1.0          flowCore_2.24.0
    ## [52] stringr_1.6.0         parallel_4.6.0        BiocManager_1.30.27
    ## [55] matrixStats_1.5.0     vctrs_0.7.3           jsonlite_2.0.0
    ## [58] cytolib_2.24.0        bookdown_0.46         IRanges_2.46.0
    ## [61] GetoptLong_1.1.1      S4Vectors_0.50.0      bit64_4.8.0
    ## [64] clue_0.3-68           Rgraphviz_2.56.0      magick_2.9.1
    ## [67] foreach_1.5.2         jquerylib_0.1.4       hexbin_1.28.5
    ## [70] glue_1.8.1            codetools_0.2-20      stringi_1.8.7
    ## [73] gtable_0.3.6          shape_1.4.6.1         ggcyto_1.40.0
    ## [76] ComplexHeatmap_2.28.0 tibble_3.3.1          pillar_1.11.1
    ## [79] rappdirs_0.3.4        htmltools_0.5.9       graph_1.90.0
    ## [82] circlize_0.4.18       R6_2.6.1              dbplyr_2.5.2
    ## [85] httr2_1.2.2           doParallel_1.0.17     evaluate_1.0.5
    ## [88] flowWorkspace_4.24.0  lattice_0.22-9        Biobase_2.72.0
    ## [91] png_0.1-9             memoise_2.0.1         bslib_0.10.0
    ## [94] Rcpp_1.1.1-1.1        gridExtra_2.3         xfun_0.57
    ## [97] zoo_1.8-15            pkgconfig_2.0.3       GlobalOptions_0.1.4