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] ggplot2_4.0.3       reshape2_1.4.5      CytoPipeline_1.13.1
## [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_2.1.8.3       RSQLite_3.53.3        magrittr_2.0.5       
## [16] compiler_4.6.1        rlang_1.3.0           sass_0.4.10          
## [19] tools_4.6.1           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_3.0.3           purrr_1.2.2          
## [31] RProtoBufLib_2.25.0   BiocGenerics_0.59.12  PeacoQC_1.23.0       
## [34] grid_4.6.1            stats4_4.6.1          flowAI_1.43.0        
## [37] colorspace_2.1-3      scales_1.4.0          iterators_1.0.14     
## [40] tinytex_0.60          dichromat_2.0-1       cli_3.6.6            
## [43] rmarkdown_2.31        crayon_1.5.3          ncdfFlow_2.59.1      
## [46] generics_0.1.4        otel_0.2.0            rjson_0.2.23         
## [49] DBI_1.3.0             cachem_1.1.0          flowCore_2.25.1      
## [52] stringr_1.6.0         parallel_4.6.1        BiocManager_1.30.27  
## [55] matrixStats_1.5.0     vctrs_0.7.3           jsonlite_2.0.0       
## [58] cytolib_2.25.0        bookdown_0.47         IRanges_2.47.2       
## [61] GetoptLong_1.1.1      S4Vectors_0.51.6      bit64_4.8.2          
## [64] clue_0.3-68           Rgraphviz_2.57.0      magick_2.9.1         
## [67] foreach_1.5.2         jquerylib_0.1.4       hexbin_1.28.6        
## [70] glue_1.8.1            codetools_0.2-20      stringi_1.8.9        
## [73] gtable_0.3.6          shape_1.4.6.1         ggcyto_1.41.1        
## [76] ComplexHeatmap_2.29.0 tibble_3.3.1          pillar_1.11.1        
## [79] htmltools_0.5.9       graph_1.91.0          circlize_0.4.18      
## [82] R6_2.6.1              dbplyr_2.6.0          httr2_1.3.0          
## [85] doParallel_1.0.17     evaluate_1.0.5        flowWorkspace_4.25.1 
## [88] lattice_0.22-9        Biobase_2.73.2        png_0.1-9            
## [91] memoise_2.0.1         bslib_0.12.0          Rcpp_1.1.2           
## [94] gridExtra_2.3.1       xfun_0.60             zoo_1.9-0            
## [97] pkgconfig_2.0.3       GlobalOptions_0.1.4