# Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps and Laurent Gatto

#### 24 October 2023

#### 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 1.2.0

# 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 4.3.1 (2023-06-16)
    ## Platform: x86_64-pc-linux-gnu (64-bit)
    ## Running under: Ubuntu 22.04.3 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
    ## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
    ##
    ## 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_1.1.3       CytoPipelineGUI_1.0.0 CytoPipeline_1.2.0
    ## [4] BiocStyle_2.30.0
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] DBI_1.1.3             gridExtra_2.3         rlang_1.1.1
    ##   [4] magrittr_2.0.3        clue_0.3-65           GetoptLong_1.0.5
    ##   [7] matrixStats_1.0.0     compiler_4.3.1        RSQLite_2.3.1
    ##  [10] png_0.1-8             vctrs_0.6.4           reshape2_1.4.4
    ##  [13] stringr_1.5.0         pkgconfig_2.0.3       shape_1.4.6
    ##  [16] crayon_1.5.2          fastmap_1.1.1         magick_2.8.1
    ##  [19] dbplyr_2.3.4          ellipsis_0.3.2        labeling_0.4.3
    ##  [22] utf8_1.2.4            promises_1.2.1        ncdfFlow_2.48.0
    ##  [25] rmarkdown_2.25        graph_1.80.0          purrr_1.0.2
    ##  [28] bit_4.0.5             xfun_0.40             zlibbioc_1.48.0
    ##  [31] cachem_1.0.8          jsonlite_1.8.7        flowWorkspace_4.14.0
    ##  [34] blob_1.2.4            later_1.3.1           parallel_4.3.1
    ##  [37] cluster_2.1.4         R6_2.5.1              bslib_0.5.1
    ##  [40] stringi_1.7.12        RColorBrewer_1.1-3    jquerylib_0.1.4
    ##  [43] Rcpp_1.0.11           bookdown_0.36         iterators_1.0.14
    ##  [46] knitr_1.44            zoo_1.8-12            IRanges_2.36.0
    ##  [49] flowCore_2.14.0       httpuv_1.6.12         tidyselect_1.2.0
    ##  [52] yaml_2.3.7            doParallel_1.0.17     codetools_0.2-19
    ##  [55] curl_5.1.0            lattice_0.22-5        tibble_3.2.1
    ##  [58] plyr_1.8.9            Biobase_2.62.0        shiny_1.7.5.1
    ##  [61] withr_2.5.1           evaluate_0.22         BiocFileCache_2.10.0
    ##  [64] circlize_0.4.15       pillar_1.9.0          BiocManager_1.30.22
    ##  [67] filelock_1.0.2        foreach_1.5.2         flowAI_1.32.0
    ##  [70] stats4_4.3.1          generics_0.1.3        diagram_1.6.5
    ##  [73] S4Vectors_0.40.0      ggplot2_3.4.4         munsell_0.5.0
    ##  [76] ggcyto_1.30.0         scales_1.2.1          xtable_1.8-4
    ##  [79] PeacoQC_1.12.0        glue_1.6.2            changepoint_2.2.4
    ##  [82] tools_4.3.1           hexbin_1.28.3         data.table_1.14.8
    ##  [85] XML_3.99-0.14         grid_4.3.1            RProtoBufLib_2.14.0
    ##  [88] colorspace_2.1-0      cli_3.6.1             fansi_1.0.5
    ##  [91] cytolib_2.14.0        ComplexHeatmap_2.18.0 dplyr_1.1.3
    ##  [94] Rgraphviz_2.46.0      gtable_0.3.4          sass_0.4.7
    ##  [97] digest_0.6.33         BiocGenerics_0.48.0   farver_2.1.1
    ## [100] rjson_0.2.21          memoise_2.0.1         htmltools_0.5.6.1
    ## [103] lifecycle_1.0.3       httr_1.4.7            GlobalOptions_0.1.2
    ## [106] mime_0.12             bit64_4.0.5