# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 7 October 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 1.9.4

# 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 (2025-09-10 r88807)
    ## 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_4.0.0      reshape2_1.4.4     CytoPipeline_1.9.4 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] S7_0.2.0              fastmap_1.2.0         BiocFileCache_2.99.6
    ## [10] XML_3.99-0.19         digest_0.6.37         lifecycle_1.0.4
    ## [13] cluster_2.1.8.1       RSQLite_2.4.3         magrittr_2.0.4
    ## [16] compiler_4.5.1        rlang_1.1.6           sass_0.4.10
    ## [19] tools_4.5.1           yaml_2.3.10           data.table_1.17.8
    ## [22] knitr_1.50            labeling_0.4.3        bit_4.6.0
    ## [25] curl_7.0.0            diagram_1.6.5         plyr_1.8.9
    ## [28] RColorBrewer_1.1-3    withr_3.0.2           purrr_1.1.0
    ## [31] RProtoBufLib_2.21.0   BiocGenerics_0.55.1   PeacoQC_1.19.0
    ## [34] grid_4.5.1            stats4_4.5.1          flowAI_1.39.0
    ## [37] colorspace_2.1-2      scales_1.4.0          iterators_1.0.14
    ## [40] tinytex_0.57          dichromat_2.0-0.1     cli_3.6.5
    ## [43] rmarkdown_2.30        crayon_1.5.3          ncdfFlow_2.55.0
    ## [46] generics_0.1.4        rjson_0.2.23          DBI_1.2.3
    ## [49] cachem_1.1.0          flowCore_2.21.0       stringr_1.5.2
    ## [52] parallel_4.5.1        BiocManager_1.30.26   matrixStats_1.5.0
    ## [55] vctrs_0.6.5           jsonlite_2.0.0        cytolib_2.21.0
    ## [58] bookdown_0.45         IRanges_2.43.5        GetoptLong_1.0.5
    ## [61] S4Vectors_0.47.4      bit64_4.6.0-1         clue_0.3-66
    ## [64] Rgraphviz_2.53.0      magick_2.9.0          foreach_1.5.2
    ## [67] jquerylib_0.1.4       hexbin_1.28.5         glue_1.8.0
    ## [70] codetools_0.2-20      stringi_1.8.7         gtable_0.3.6
    ## [73] shape_1.4.6.1         ggcyto_1.37.1         ComplexHeatmap_2.25.2
    ## [76] tibble_3.3.0          pillar_1.11.1         rappdirs_0.3.3
    ## [79] htmltools_0.5.8.1     graph_1.87.0          circlize_0.4.16
    ## [82] R6_2.6.1              dbplyr_2.5.1          httr2_1.2.1
    ## [85] doParallel_1.0.17     evaluate_1.0.5        flowWorkspace_4.21.0
    ## [88] lattice_0.22-7        Biobase_2.69.1        png_0.1-8
    ## [91] memoise_2.0.1         bslib_0.9.0           Rcpp_1.1.0
    ## [94] gridExtra_2.3         xfun_0.53             zoo_1.8-14
    ## [97] pkgconfig_2.0.3       GlobalOptions_0.1.2