# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 29 October 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: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.1 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
    ## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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_1.3.0       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_2.28
    ##  [25] graph_1.84.0          tinytex_0.53          purrr_1.0.2
    ##  [28] bit_4.5.0             xfun_0.48             zlibbioc_1.52.0
    ##  [31] cachem_1.1.0          jsonlite_1.8.9        flowWorkspace_4.18.0
    ##  [34] blob_1.2.4            highr_0.11            later_1.3.2
    ##  [37] parallel_4.4.1        cluster_2.1.6         R6_2.5.1
    ##  [40] bslib_0.8.0           stringi_1.8.4         RColorBrewer_1.1-3
    ##  [43] jquerylib_0.1.4       Rcpp_1.0.13           bookdown_0.41
    ##  [46] iterators_1.0.14      knitr_1.48            zoo_1.8-12
    ##  [49] IRanges_2.40.0        flowCore_2.18.0       httpuv_1.6.15
    ##  [52] tidyselect_1.2.1      yaml_2.3.10           doParallel_1.0.17
    ##  [55] codetools_0.2-20      curl_5.2.3            lattice_0.22-6
    ##  [58] tibble_3.2.1          plyr_1.8.9            Biobase_2.66.0
    ##  [61] shiny_1.9.1           withr_3.0.2           evaluate_1.0.1
    ##  [64] BiocFileCache_2.14.0  circlize_0.4.16       pillar_1.9.0
    ##  [67] BiocManager_1.30.25   filelock_1.0.3        foreach_1.5.2
    ##  [70] flowAI_1.36.0         stats4_4.4.1          generics_0.1.3
    ##  [73] diagram_1.6.5         S4Vectors_0.44.0      ggplot2_3.5.1
    ##  [76] munsell_0.5.1         ggcyto_1.34.0         scales_1.3.0
    ##  [79] xtable_1.8-4          PeacoQC_1.16.0        glue_1.8.0
    ##  [82] changepoint_2.2.4     tools_4.4.1           hexbin_1.28.4
    ##  [85] data.table_1.16.2     XML_3.99-0.17         grid_4.4.1
    ##  [88] RProtoBufLib_2.18.0   colorspace_2.1-1      cli_3.6.3
    ##  [91] fansi_1.0.6           cytolib_2.18.0        ComplexHeatmap_2.22.0
    ##  [94] dplyr_1.1.4           Rgraphviz_2.50.0      gtable_0.3.6
    ##  [97] sass_0.4.9            digest_0.6.37         BiocGenerics_0.52.0
    ## [100] rjson_0.2.23          farver_2.1.2          memoise_2.0.1
    ## [103] htmltools_0.5.8.1     lifecycle_1.0.4       httr_1.4.7
    ## [106] GlobalOptions_0.1.2   mime_0.12             bit64_4.5.2