# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 1 May 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 1.4.0

# 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 4.4.0 alpha (2024-03-27 r86216)
    ## Platform: aarch64-apple-darwin20
    ## Running under: macOS Ventura 13.6.5
    ##
    ## 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] en_US.UTF-8/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_3.5.0      reshape2_1.4.4     CytoPipeline_1.4.0 BiocStyle_2.32.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] changepoint_2.2.4     tidyselect_1.2.1      farver_2.1.1
    ##  [4] dplyr_1.1.4           blob_1.2.4            filelock_1.0.3
    ##  [7] fastmap_1.1.1         BiocFileCache_2.12.0  XML_3.99-0.16.1
    ## [10] digest_0.6.35         lifecycle_1.0.4       cluster_2.1.6
    ## [13] RSQLite_2.3.5         magrittr_2.0.3        compiler_4.4.0
    ## [16] rlang_1.1.3           sass_0.4.9            tools_4.4.0
    ## [19] utf8_1.2.4            yaml_2.3.8            data.table_1.15.4
    ## [22] knitr_1.45            labeling_0.4.3        bit_4.0.5
    ## [25] curl_5.2.1            diagram_1.6.5         plyr_1.8.9
    ## [28] RColorBrewer_1.1-3    withr_3.0.0           purrr_1.0.2
    ## [31] RProtoBufLib_2.16.0   BiocGenerics_0.50.0   PeacoQC_1.14.0
    ## [34] grid_4.4.0            stats4_4.4.0          fansi_1.0.6
    ## [37] flowAI_1.34.0         colorspace_2.1-0      scales_1.3.0
    ## [40] iterators_1.0.14      cli_3.6.2             rmarkdown_2.26
    ## [43] crayon_1.5.2          ncdfFlow_2.50.0       generics_0.1.3
    ## [46] httr_1.4.7            rjson_0.2.21          DBI_1.2.2
    ## [49] cachem_1.0.8          flowCore_2.16.0       stringr_1.5.1
    ## [52] zlibbioc_1.50.0       parallel_4.4.0        BiocManager_1.30.22
    ## [55] matrixStats_1.2.0     vctrs_0.6.5           jsonlite_1.8.8
    ## [58] cytolib_2.16.0        bookdown_0.38         IRanges_2.38.0
    ## [61] GetoptLong_1.0.5      S4Vectors_0.42.0      bit64_4.0.5
    ## [64] clue_0.3-65           Rgraphviz_2.48.0      magick_2.8.3
    ## [67] foreach_1.5.2         jquerylib_0.1.4       hexbin_1.28.3
    ## [70] glue_1.7.0            codetools_0.2-19      stringi_1.8.3
    ## [73] gtable_0.3.4          shape_1.4.6.1         ggcyto_1.32.0
    ## [76] ComplexHeatmap_2.20.0 munsell_0.5.0         tibble_3.2.1
    ## [79] pillar_1.9.0          htmltools_0.5.8       graph_1.82.0
    ## [82] circlize_0.4.16       R6_2.5.1              dbplyr_2.5.0
    ## [85] doParallel_1.0.17     evaluate_0.23         flowWorkspace_4.16.0
    ## [88] lattice_0.22-6        Biobase_2.64.0        highr_0.10
    ## [91] png_0.1-8             memoise_2.0.1         bslib_0.6.2
    ## [94] Rcpp_1.0.12           gridExtra_2.3         xfun_0.43
    ## [97] zoo_1.8-12            pkgconfig_2.0.3       GlobalOptions_0.1.2