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 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.24-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## 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_1.3.2        CytoPipelineGUI_1.11.1 CytoPipeline_1.13.1   
## [4] BiocStyle_2.41.0      
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.3.0             gridExtra_2.3.1       httr2_1.3.0          
##   [4] rlang_1.3.0           magrittr_2.0.5        clue_0.3-68          
##   [7] GetoptLong_1.1.1      otel_0.2.0            matrixStats_1.5.0    
##  [10] compiler_4.6.1        RSQLite_3.53.3        png_0.1-9            
##  [13] vctrs_0.7.3           reshape2_1.4.5        stringr_1.6.0        
##  [16] pkgconfig_2.0.3       shape_1.4.6.1         crayon_1.5.3         
##  [19] fastmap_1.2.0         magick_2.9.1          dbplyr_2.6.0         
##  [22] labeling_0.4.3        promises_1.5.0        ncdfFlow_2.59.1      
##  [25] rmarkdown_2.31        graph_1.91.0          tinytex_0.60         
##  [28] purrr_1.2.2           bit_4.6.0             xfun_0.60            
##  [31] cachem_1.1.0          jsonlite_2.0.0        flowWorkspace_4.25.1 
##  [34] blob_1.3.0            later_1.4.8           parallel_4.6.1       
##  [37] cluster_2.1.8.3       R6_2.6.1              bslib_0.12.0         
##  [40] stringi_1.8.9         RColorBrewer_1.1-3    jquerylib_0.1.4      
##  [43] Rcpp_1.1.2            bookdown_0.47         iterators_1.0.14     
##  [46] knitr_1.51            zoo_1.9-0             IRanges_2.47.2       
##  [49] flowCore_2.25.1       httpuv_1.6.17         tidyselect_1.2.1     
##  [52] dichromat_2.0-1       yaml_2.3.12           doParallel_1.0.17    
##  [55] codetools_0.2-20      curl_7.1.0            lattice_0.22-9       
##  [58] tibble_3.3.1          plyr_1.8.9            Biobase_2.73.2       
##  [61] shiny_1.14.0          withr_3.0.3           S7_0.2.2             
##  [64] evaluate_1.0.5        BiocFileCache_3.3.0   circlize_0.4.18      
##  [67] pillar_1.11.1         BiocManager_1.30.27   filelock_1.0.3       
##  [70] foreach_1.5.2         flowAI_1.43.0         stats4_4.6.1         
##  [73] generics_0.1.4        S4Vectors_0.51.6      ggplot2_4.0.3        
##  [76] ggcyto_1.41.1         scales_1.4.0          xtable_1.8-8         
##  [79] PeacoQC_1.23.0        glue_1.8.1            changepoint_2.3      
##  [82] tools_4.6.1           hexbin_1.28.6         data.table_1.18.4    
##  [85] XML_3.99-0.23         grid_4.6.1            RProtoBufLib_2.25.0  
##  [88] colorspace_2.1-3      cli_3.6.6             cytolib_2.25.0       
##  [91] ComplexHeatmap_2.29.0 dplyr_1.2.1           Rgraphviz_2.57.0     
##  [94] gtable_0.3.6          sass_0.4.10           digest_0.6.39        
##  [97] BiocGenerics_0.59.12  rjson_0.2.23          farver_2.1.2         
## [100] memoise_2.0.1         htmltools_0.5.9       lifecycle_1.0.5      
## [103] GlobalOptions_0.1.4   mime_0.13             bit64_4.8.2