# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 8 November 2024

#### 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 1.6.0

# 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 4.4.1 (2024-06-14)
    ## Platform: aarch64-apple-darwin20
    ## Running under: macOS Ventura 13.6.7
    ##
    ## Matrix products: default
    ## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
    ##
    ## 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] patchwork_1.3.0       CytoPipelineGUI_1.4.0 CytoPipeline_1.6.0
    ## [4] BiocStyle_2.34.0
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] DBI_1.2.3             gridExtra_2.3         rlang_1.1.4
    ##   [4] magrittr_2.0.3        clue_0.3-65           GetoptLong_1.0.5
    ##   [7] matrixStats_1.4.1     compiler_4.4.1        RSQLite_2.3.7
    ##  [10] png_0.1-8             vctrs_0.6.5           reshape2_1.4.4
    ##  [13] stringr_1.5.1         pkgconfig_2.0.3       shape_1.4.6.1
    ##  [16] crayon_1.5.3          fastmap_1.2.0         magick_2.8.5
    ##  [19] dbplyr_2.5.0          labeling_0.4.3        utf8_1.2.4
    ##  [22] promises_1.3.0        ncdfFlow_2.52.0       rmarkdown_2.29
    ##  [25] graph_1.84.0          tinytex_0.54          purrr_1.0.2
    ##  [28] bit_4.5.0             xfun_0.49             zlibbioc_1.52.0
    ##  [31] cachem_1.1.0          jsonlite_1.8.9        flowWorkspace_4.18.0
    ##  [34] blob_1.2.4            later_1.3.2           parallel_4.4.1
    ##  [37] cluster_2.1.6         R6_2.5.1              bslib_0.8.0
    ##  [40] stringi_1.8.4         RColorBrewer_1.1-3    jquerylib_0.1.4
    ##  [43] Rcpp_1.0.13-1         bookdown_0.41         iterators_1.0.14
    ##  [46] knitr_1.49            zoo_1.8-12            IRanges_2.40.0
    ##  [49] flowCore_2.18.0       httpuv_1.6.15         tidyselect_1.2.1
    ##  [52] yaml_2.3.10           doParallel_1.0.17     codetools_0.2-20
    ##  [55] curl_6.0.0            lattice_0.22-6        tibble_3.2.1
    ##  [58] plyr_1.8.9            Biobase_2.66.0        shiny_1.9.1
    ##  [61] withr_3.0.2           evaluate_1.0.1        BiocFileCache_2.14.0
    ##  [64] circlize_0.4.16       pillar_1.9.0          BiocManager_1.30.25
    ##  [67] filelock_1.0.3        foreach_1.5.2         flowAI_1.36.0
    ##  [70] stats4_4.4.1          generics_0.1.3        diagram_1.6.5
    ##  [73] S4Vectors_0.44.0      ggplot2_3.5.1         munsell_0.5.1
    ##  [76] ggcyto_1.34.0         scales_1.3.0          xtable_1.8-4
    ##  [79] PeacoQC_1.16.0        glue_1.8.0            changepoint_2.3
    ##  [82] tools_4.4.1           hexbin_1.28.4         data.table_1.16.2
    ##  [85] XML_3.99-0.17         grid_4.4.1            RProtoBufLib_2.18.0
    ##  [88] colorspace_2.1-1      cli_3.6.3             fansi_1.0.6
    ##  [91] cytolib_2.18.0        ComplexHeatmap_2.22.0 dplyr_1.1.4
    ##  [94] Rgraphviz_2.50.0      gtable_0.3.6          sass_0.4.9
    ##  [97] digest_0.6.37         BiocGenerics_0.52.0   rjson_0.2.23
    ## [100] farver_2.1.2          memoise_2.0.1         htmltools_0.5.8.1
    ## [103] lifecycle_1.0.4       httr_1.4.7            GlobalOptions_0.1.2
    ## [106] mime_0.12             bit64_4.5.2