# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 26 August 2025

#### 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 1.9.0

# 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 4.5.1 Patched (2025-06-14 r88325)
    ## Platform: aarch64-apple-darwin20
    ## Running under: macOS Ventura 13.7.7
    ##
    ## Matrix products: default
    ## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/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_3.5.2      reshape2_1.4.4     CytoPipeline_1.9.0 BiocStyle_2.37.1
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] changepoint_2.3       tidyselect_1.2.1      dplyr_1.1.4
    ##  [4] farver_2.1.2          blob_1.2.4            filelock_1.0.3
    ##  [7] fastmap_1.2.0         BiocFileCache_2.99.6  XML_3.99-0.19
    ## [10] digest_0.6.37         lifecycle_1.0.4       cluster_2.1.8.1
    ## [13] RSQLite_2.4.3         magrittr_2.0.3        compiler_4.5.1
    ## [16] rlang_1.1.6           sass_0.4.10           tools_4.5.1
    ## [19] yaml_2.3.10           data.table_1.17.8     knitr_1.50
    ## [22] labeling_0.4.3        bit_4.6.0             curl_7.0.0
    ## [25] diagram_1.6.5         plyr_1.8.9            RColorBrewer_1.1-3
    ## [28] withr_3.0.2           purrr_1.1.0           RProtoBufLib_2.21.0
    ## [31] BiocGenerics_0.55.1   PeacoQC_1.19.0        grid_4.5.1
    ## [34] stats4_4.5.1          flowAI_1.39.0         colorspace_2.1-1
    ## [37] scales_1.4.0          iterators_1.0.14      tinytex_0.57
    ## [40] dichromat_2.0-0.1     cli_3.6.5             rmarkdown_2.29
    ## [43] crayon_1.5.3          ncdfFlow_2.55.0       generics_0.1.4
    ## [46] rjson_0.2.23          DBI_1.2.3             cachem_1.1.0
    ## [49] flowCore_2.21.0       stringr_1.5.1         parallel_4.5.1
    ## [52] BiocManager_1.30.26   matrixStats_1.5.0     vctrs_0.6.5
    ## [55] jsonlite_2.0.0        cytolib_2.21.0        bookdown_0.44
    ## [58] IRanges_2.43.0        GetoptLong_1.0.5      S4Vectors_0.47.0
    ## [61] bit64_4.6.0-1         clue_0.3-66           Rgraphviz_2.53.0
    ## [64] magick_2.8.7          foreach_1.5.2         jquerylib_0.1.4
    ## [67] hexbin_1.28.5         glue_1.8.0            codetools_0.2-20
    ## [70] stringi_1.8.7         gtable_0.3.6          shape_1.4.6.1
    ## [73] ggcyto_1.37.0         ComplexHeatmap_2.25.2 tibble_3.3.0
    ## [76] pillar_1.11.0         rappdirs_0.3.3        htmltools_0.5.8.1
    ## [79] graph_1.87.0          circlize_0.4.16       R6_2.6.1
    ## [82] dbplyr_2.5.0          httr2_1.2.1           doParallel_1.0.17
    ## [85] evaluate_1.0.4        flowWorkspace_4.21.0  lattice_0.22-7
    ## [88] Biobase_2.69.0        png_0.1-8             memoise_2.0.1
    ## [91] bslib_0.9.0           Rcpp_1.1.0            gridExtra_2.3
    ## [94] xfun_0.53             zoo_1.8-14            pkgconfig_2.0.3
    ## [97] GlobalOptions_0.1.2