Date: 2025-10-29

# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 29 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 1.10.0

# 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 (2025-08-23 r88802)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
    ## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_GB              LC_COLLATE=C
    ##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
    ##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
    ##  [9] LC_ADDRESS=C               LC_TELEPHONE=C
    ## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
    ##
    ## time zone: America/New_York
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] patchwork_1.3.2       CytoPipelineGUI_1.8.0 CytoPipeline_1.10.0
    ## [4] BiocStyle_2.38.0
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] DBI_1.2.3             gridExtra_2.3         httr2_1.2.1
    ##   [4] rlang_1.1.6           magrittr_2.0.4        clue_0.3-66
    ##   [7] GetoptLong_1.0.5      otel_0.2.0            matrixStats_1.5.0
    ##  [10] compiler_4.5.1        RSQLite_2.4.3         png_0.1-8
    ##  [13] vctrs_0.6.5           reshape2_1.4.4        stringr_1.5.2
    ##  [16] pkgconfig_2.0.3       shape_1.4.6.1         crayon_1.5.3
    ##  [19] fastmap_1.2.0         magick_2.9.0          dbplyr_2.5.1
    ##  [22] labeling_0.4.3        promises_1.4.0        ncdfFlow_2.56.0
    ##  [25] rmarkdown_2.30        graph_1.88.0          tinytex_0.57
    ##  [28] purrr_1.1.0           bit_4.6.0             xfun_0.53
    ##  [31] cachem_1.1.0          jsonlite_2.0.0        flowWorkspace_4.22.0
    ##  [34] blob_1.2.4            later_1.4.4           parallel_4.5.1
    ##  [37] cluster_2.1.8.1       R6_2.6.1              bslib_0.9.0
    ##  [40] stringi_1.8.7         RColorBrewer_1.1-3    jquerylib_0.1.4
    ##  [43] Rcpp_1.1.0            bookdown_0.45         iterators_1.0.14
    ##  [46] knitr_1.50            zoo_1.8-14            IRanges_2.44.0
    ##  [49] flowCore_2.22.0       httpuv_1.6.16         tidyselect_1.2.1
    ##  [52] dichromat_2.0-0.1     yaml_2.3.10           doParallel_1.0.17
    ##  [55] codetools_0.2-20      curl_7.0.0            lattice_0.22-7
    ##  [58] tibble_3.3.0          plyr_1.8.9            Biobase_2.70.0
    ##  [61] shiny_1.11.1          withr_3.0.2           S7_0.2.0
    ##  [64] evaluate_1.0.5        BiocFileCache_3.0.0   circlize_0.4.16
    ##  [67] pillar_1.11.1         BiocManager_1.30.26   filelock_1.0.3
    ##  [70] foreach_1.5.2         flowAI_1.40.0         stats4_4.5.1
    ##  [73] generics_0.1.4        S4Vectors_0.48.0      ggplot2_4.0.0
    ##  [76] ggcyto_1.38.0         scales_1.4.0          xtable_1.8-4
    ##  [79] PeacoQC_1.20.0        glue_1.8.0            changepoint_2.3
    ##  [82] tools_4.5.1           hexbin_1.28.5         data.table_1.17.8
    ##  [85] XML_3.99-0.19         grid_4.5.1            RProtoBufLib_2.22.0
    ##  [88] colorspace_2.1-2      cli_3.6.5             rappdirs_0.3.3
    ##  [91] cytolib_2.22.0        ComplexHeatmap_2.26.0 dplyr_1.1.4
    ##  [94] Rgraphviz_2.54.0      gtable_0.3.6          sass_0.4.10
    ##  [97] digest_0.6.37         BiocGenerics_0.56.0   rjson_0.2.23
    ## [100] farver_2.1.2          memoise_2.0.1         htmltools_0.5.8.1
    ## [103] lifecycle_1.0.4       GlobalOptions_0.1.2   mime_0.13
    ## [106] bit64_4.6.0-1