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 4.5.0 RC (2025-04-04 r88126)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.21-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_1.3.0       CytoPipelineGUI_1.6.0 CytoPipeline_1.8.0   
## [4] BiocStyle_2.36.0     
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3             gridExtra_2.3         rlang_1.1.6          
##   [4] magrittr_2.0.3        clue_0.3-66           GetoptLong_1.0.5     
##   [7] matrixStats_1.5.0     compiler_4.5.0        RSQLite_2.3.9        
##  [10] png_0.1-8             vctrs_0.6.5           reshape2_1.4.4       
##  [13] stringr_1.5.1         pkgconfig_2.0.3       shape_1.4.6.1        
##  [16] crayon_1.5.3          fastmap_1.2.0         dbplyr_2.5.0         
##  [19] magick_2.8.6          labeling_0.4.3        promises_1.3.2       
##  [22] ncdfFlow_2.54.0       rmarkdown_2.29        graph_1.86.0         
##  [25] tinytex_0.57          purrr_1.0.4           bit_4.6.0            
##  [28] xfun_0.52             cachem_1.1.0          jsonlite_2.0.0       
##  [31] flowWorkspace_4.20.0  blob_1.2.4            later_1.4.2          
##  [34] parallel_4.5.0        cluster_2.1.8.1       R6_2.6.1             
##  [37] bslib_0.9.0           stringi_1.8.7         RColorBrewer_1.1-3   
##  [40] jquerylib_0.1.4       Rcpp_1.0.14           bookdown_0.43        
##  [43] iterators_1.0.14      knitr_1.50            zoo_1.8-14           
##  [46] IRanges_2.42.0        flowCore_2.20.0       httpuv_1.6.15        
##  [49] tidyselect_1.2.1      yaml_2.3.10           doParallel_1.0.17    
##  [52] codetools_0.2-20      curl_6.2.2            lattice_0.22-7       
##  [55] tibble_3.2.1          plyr_1.8.9            Biobase_2.68.0       
##  [58] shiny_1.10.0          withr_3.0.2           evaluate_1.0.3       
##  [61] BiocFileCache_2.16.0  circlize_0.4.16       pillar_1.10.2        
##  [64] BiocManager_1.30.25   filelock_1.0.3        foreach_1.5.2        
##  [67] flowAI_1.38.0         stats4_4.5.0          generics_0.1.3       
##  [70] diagram_1.6.5         S4Vectors_0.46.0      ggplot2_3.5.2        
##  [73] munsell_0.5.1         ggcyto_1.36.0         scales_1.3.0         
##  [76] xtable_1.8-4          PeacoQC_1.18.0        glue_1.8.0           
##  [79] changepoint_2.3       tools_4.5.0           hexbin_1.28.5        
##  [82] data.table_1.17.0     XML_3.99-0.18         grid_4.5.0           
##  [85] RProtoBufLib_2.20.0   colorspace_2.1-1      cli_3.6.4            
##  [88] cytolib_2.20.0        ComplexHeatmap_2.24.0 dplyr_1.1.4          
##  [91] Rgraphviz_2.52.0      gtable_0.3.6          sass_0.4.10          
##  [94] digest_0.6.37         BiocGenerics_0.54.0   rjson_0.2.23         
##  [97] farver_2.1.2          memoise_2.0.1         htmltools_0.5.8.1    
## [100] lifecycle_1.0.4       httr_1.4.7            GlobalOptions_0.1.2  
## [103] mime_0.13             bit64_4.6.0-1