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 (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-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_1.7.2 CytoPipeline_1.9.4   
## [4] BiocStyle_2.37.1     
## 
## 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      matrixStats_1.5.0     compiler_4.5.1       
##  [10] RSQLite_2.4.3         png_0.1-8             vctrs_0.6.5          
##  [13] reshape2_1.4.4        stringr_1.5.2         pkgconfig_2.0.3      
##  [16] shape_1.4.6.1         crayon_1.5.3          fastmap_1.2.0        
##  [19] magick_2.9.0          dbplyr_2.5.1          labeling_0.4.3       
##  [22] promises_1.3.3        ncdfFlow_2.55.0       rmarkdown_2.30       
##  [25] graph_1.87.0          tinytex_0.57          purrr_1.1.0          
##  [28] bit_4.6.0             xfun_0.53             cachem_1.1.0         
##  [31] jsonlite_2.0.0        flowWorkspace_4.21.0  blob_1.2.4           
##  [34] later_1.4.4           parallel_4.5.1        cluster_2.1.8.1      
##  [37] R6_2.6.1              bslib_0.9.0           stringi_1.8.7        
##  [40] RColorBrewer_1.1-3    jquerylib_0.1.4       Rcpp_1.1.0           
##  [43] bookdown_0.44         iterators_1.0.14      knitr_1.50           
##  [46] zoo_1.8-14            IRanges_2.43.5        flowCore_2.21.0      
##  [49] httpuv_1.6.16         tidyselect_1.2.1      dichromat_2.0-0.1    
##  [52] yaml_2.3.10           doParallel_1.0.17     codetools_0.2-20     
##  [55] curl_7.0.0            lattice_0.22-7        tibble_3.3.0         
##  [58] plyr_1.8.9            Biobase_2.69.1        shiny_1.11.1         
##  [61] withr_3.0.2           S7_0.2.0              evaluate_1.0.5       
##  [64] BiocFileCache_2.99.6  circlize_0.4.16       pillar_1.11.1        
##  [67] BiocManager_1.30.26   filelock_1.0.3        foreach_1.5.2        
##  [70] flowAI_1.39.0         stats4_4.5.1          generics_0.1.4       
##  [73] S4Vectors_0.47.4      ggplot2_4.0.0         ggcyto_1.37.1        
##  [76] scales_1.4.0          xtable_1.8-4          PeacoQC_1.19.0       
##  [79] glue_1.8.0            changepoint_2.3       tools_4.5.1          
##  [82] hexbin_1.28.5         data.table_1.17.8     XML_3.99-0.19        
##  [85] grid_4.5.1            RProtoBufLib_2.21.0   colorspace_2.1-2     
##  [88] cli_3.6.5             rappdirs_0.3.3        cytolib_2.21.0       
##  [91] ComplexHeatmap_2.25.2 dplyr_1.1.4           Rgraphviz_2.53.0     
##  [94] gtable_0.3.6          sass_0.4.10           digest_0.6.37        
##  [97] BiocGenerics_0.55.1   rjson_0.2.23          farver_2.1.2         
## [100] memoise_2.0.1         htmltools_0.5.8.1     lifecycle_1.0.4      
## [103] GlobalOptions_0.1.2   mime_0.13             bit64_4.6.0-1