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 4.5.1 Patched (2025-09-10 r88807)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C/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] patchwork_1.3.2       CytoPipelineGUI_1.8.0 CytoPipeline_1.10.0  
## [4] BiocStyle_2.38.0     
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3             gridExtra_2.3         httr2_1.2.1          
##   [4] rlang_1.1.6           magrittr_2.0.4        clue_0.3-66          
##   [7] GetoptLong_1.0.5      otel_0.2.0            matrixStats_1.5.0    
##  [10] compiler_4.5.1        RSQLite_2.4.3         png_0.1-8            
##  [13] vctrs_0.6.5           reshape2_1.4.4        stringr_1.5.2        
##  [16] pkgconfig_2.0.3       shape_1.4.6.1         crayon_1.5.3         
##  [19] fastmap_1.2.0         magick_2.9.0          dbplyr_2.5.1         
##  [22] labeling_0.4.3        promises_1.4.0        ncdfFlow_2.56.0      
##  [25] rmarkdown_2.30        graph_1.88.0          tinytex_0.57         
##  [28] purrr_1.1.0           bit_4.6.0             xfun_0.53            
##  [31] cachem_1.1.0          jsonlite_2.0.0        flowWorkspace_4.22.0 
##  [34] blob_1.2.4            later_1.4.4           parallel_4.5.1       
##  [37] cluster_2.1.8.1       R6_2.6.1              bslib_0.9.0          
##  [40] stringi_1.8.7         RColorBrewer_1.1-3    jquerylib_0.1.4      
##  [43] Rcpp_1.1.0            bookdown_0.45         iterators_1.0.14     
##  [46] knitr_1.50            zoo_1.8-14            IRanges_2.44.0       
##  [49] flowCore_2.22.0       httpuv_1.6.16         tidyselect_1.2.1     
##  [52] dichromat_2.0-0.1     yaml_2.3.10           doParallel_1.0.17    
##  [55] codetools_0.2-20      curl_7.0.0            lattice_0.22-7       
##  [58] tibble_3.3.0          plyr_1.8.9            Biobase_2.70.0       
##  [61] shiny_1.11.1          withr_3.0.2           S7_0.2.0             
##  [64] evaluate_1.0.5        BiocFileCache_3.0.0   circlize_0.4.16      
##  [67] pillar_1.11.1         BiocManager_1.30.26   filelock_1.0.3       
##  [70] foreach_1.5.2         flowAI_1.40.0         stats4_4.5.1         
##  [73] generics_0.1.4        S4Vectors_0.48.0      ggplot2_4.0.0        
##  [76] ggcyto_1.38.0         scales_1.4.0          xtable_1.8-4         
##  [79] PeacoQC_1.20.0        glue_1.8.0            changepoint_2.3      
##  [82] tools_4.5.1           hexbin_1.28.5         data.table_1.17.8    
##  [85] XML_3.99-0.19         grid_4.5.1            RProtoBufLib_2.22.0  
##  [88] colorspace_2.1-2      cli_3.6.5             rappdirs_0.3.3       
##  [91] cytolib_2.22.0        ComplexHeatmap_2.26.0 dplyr_1.1.4          
##  [94] Rgraphviz_2.54.0      gtable_0.3.6          sass_0.4.10          
##  [97] digest_0.6.37         BiocGenerics_0.56.0   rjson_0.2.23         
## [100] farver_2.1.2          memoise_2.0.1         htmltools_0.5.8.1    
## [103] lifecycle_1.0.4       GlobalOptions_0.1.2   mime_0.13            
## [106] bit64_4.6.0-1