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