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 beta (2025-04-02 r88102)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 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] ggplot2_3.5.2      reshape2_1.4.4     CytoPipeline_1.9.0 BiocStyle_2.37.0  
## 
## loaded via a namespace (and not attached):
##  [1] changepoint_2.3       tidyselect_1.2.1      farver_2.1.2         
##  [4] dplyr_1.1.4           blob_1.2.4            filelock_1.0.3       
##  [7] fastmap_1.2.0         BiocFileCache_2.17.0  XML_3.99-0.18        
## [10] digest_0.6.37         lifecycle_1.0.4       cluster_2.1.8.1      
## [13] RSQLite_2.3.9         magrittr_2.0.3        compiler_4.5.0       
## [16] rlang_1.1.6           sass_0.4.10           tools_4.5.0          
## [19] yaml_2.3.10           data.table_1.17.0     knitr_1.50           
## [22] labeling_0.4.3        bit_4.6.0             curl_6.2.2           
## [25] diagram_1.6.5         plyr_1.8.9            RColorBrewer_1.1-3   
## [28] withr_3.0.2           purrr_1.0.4           RProtoBufLib_2.21.0  
## [31] BiocGenerics_0.55.0   PeacoQC_1.19.0        grid_4.5.0           
## [34] stats4_4.5.0          flowAI_1.39.0         colorspace_2.1-1     
## [37] scales_1.3.0          iterators_1.0.14      tinytex_0.57         
## [40] cli_3.6.4             rmarkdown_2.29        crayon_1.5.3         
## [43] ncdfFlow_2.55.0       generics_0.1.3        httr_1.4.7           
## [46] rjson_0.2.23          DBI_1.2.3             cachem_1.1.0         
## [49] flowCore_2.21.0       stringr_1.5.1         parallel_4.5.0       
## [52] BiocManager_1.30.25   matrixStats_1.5.0     vctrs_0.6.5          
## [55] jsonlite_2.0.0        cytolib_2.21.0        bookdown_0.43        
## [58] IRanges_2.43.0        GetoptLong_1.0.5      S4Vectors_0.47.0     
## [61] bit64_4.6.0-1         clue_0.3-66           Rgraphviz_2.53.0     
## [64] magick_2.8.6          foreach_1.5.2         jquerylib_0.1.4      
## [67] hexbin_1.28.5         glue_1.8.0            codetools_0.2-20     
## [70] stringi_1.8.7         gtable_0.3.6          shape_1.4.6.1        
## [73] ggcyto_1.37.0         ComplexHeatmap_2.25.0 munsell_0.5.1        
## [76] tibble_3.2.1          pillar_1.10.2         htmltools_0.5.8.1    
## [79] graph_1.87.0          circlize_0.4.16       R6_2.6.1             
## [82] dbplyr_2.5.0          doParallel_1.0.17     evaluate_1.0.3       
## [85] flowWorkspace_4.21.0  lattice_0.22-7        Biobase_2.69.0       
## [88] png_0.1-8             memoise_2.0.1         bslib_0.9.0          
## [91] Rcpp_1.0.14           gridExtra_2.3         xfun_0.52            
## [94] zoo_1.8-14            pkgconfig_2.0.3       GlobalOptions_0.1.2