# Demonstration of the CytoPipeline R package suite functionalities

# Introduction

# Background information

# Illustrating dataset

# Specifying the pipeline

# Running the pipeline

# Visualizing the results

# Comparing pipelines

# Example with two different QC methods

# Visualizing scale transformations

# Defining technical run parameters

# Session information

    ## R version 4.6.0 (2026-04-24)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.4 LTS
    ##
    ## Matrix products: default
    ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
    ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
    ##
    ## locale:
    ##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
    ##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
    ##  [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: Etc/UTC
    ## tzcode source: system (glibc)
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] ggplot2_4.0.3       reshape2_1.4.5      CytoPipeline_1.13.0
    ## [4] BiocStyle_2.41.0
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] changepoint_2.3       tidyselect_1.2.1      dplyr_1.2.1
    ##  [4] farver_2.1.2          blob_1.3.0            filelock_1.0.3
    ##  [7] S7_0.2.2              fastmap_1.2.0         BiocFileCache_3.3.0
    ## [10] XML_3.99-0.23         digest_0.6.39         lifecycle_1.0.5
    ## [13] cluster_2.1.8.2       RSQLite_3.53.1        magrittr_2.0.5
    ## [16] compiler_4.6.0        rlang_1.2.0           sass_0.4.10
    ## [19] tools_4.6.0           yaml_2.3.12           data.table_1.18.4
    ## [22] knitr_1.51            labeling_0.4.3        bit_4.6.0
    ## [25] curl_7.1.0            diagram_1.6.5         plyr_1.8.9
    ## [28] RColorBrewer_1.1-3    withr_3.0.2           purrr_1.2.2
    ## [31] RProtoBufLib_2.25.0   BiocGenerics_0.59.6   sys_3.4.3
    ## [34] PeacoQC_1.23.0        grid_4.6.0            stats4_4.6.0
    ## [37] flowAI_1.43.0         colorspace_2.1-2      scales_1.4.0
    ## [40] iterators_1.0.14      cli_3.6.6             rmarkdown_2.31
    ## [43] crayon_1.5.3          ncdfFlow_2.59.0       generics_0.1.4
    ## [46] otel_0.2.0            rjson_0.2.23          DBI_1.3.0
    ## [49] cachem_1.1.0          flowCore_2.25.1       stringr_1.6.0
    ## [52] parallel_4.6.0        BiocManager_1.30.27   matrixStats_1.5.0
    ## [55] vctrs_0.7.3           jsonlite_2.0.0        cytolib_2.25.0
    ## [58] IRanges_2.47.2        GetoptLong_1.1.1      S4Vectors_0.51.3
    ## [61] bit64_4.8.2           clue_0.3-68           Rgraphviz_2.57.0
    ## [64] maketools_1.3.2       foreach_1.5.2         jquerylib_0.1.4
    ## [67] hexbin_1.28.5         glue_1.8.1            codetools_0.2-20
    ## [70] stringi_1.8.7         gtable_0.3.6          shape_1.4.6.1
    ## [73] ggcyto_1.41.0         ComplexHeatmap_2.29.0 tibble_3.3.1
    ## [76] pillar_1.11.1         rappdirs_0.3.4        htmltools_0.5.9
    ## [79] graph_1.91.0          circlize_0.4.18       R6_2.6.1
    ## [82] dbplyr_2.5.2          httr2_1.2.2           doParallel_1.0.17
    ## [85] evaluate_1.0.5        flowWorkspace_4.25.0  lattice_0.22-9
    ## [88] Biobase_2.73.1        png_0.1-9             memoise_2.0.1
    ## [91] bslib_0.11.0          Rcpp_1.1.1-1.1        gridExtra_2.3
    ## [94] xfun_0.57             zoo_1.8-15            buildtools_1.0.0
    ## [97] pkgconfig_2.0.3       GlobalOptions_0.1.4