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] ggplot2_4.0.0      reshape2_1.4.4     CytoPipeline_1.9.4 BiocStyle_2.37.1  
## 
## loaded via a namespace (and not attached):
##  [1] changepoint_2.3       tidyselect_1.2.1      dplyr_1.1.4          
##  [4] farver_2.1.2          blob_1.2.4            filelock_1.0.3       
##  [7] S7_0.2.0              fastmap_1.2.0         BiocFileCache_2.99.6 
## [10] XML_3.99-0.19         digest_0.6.37         lifecycle_1.0.4      
## [13] cluster_2.1.8.1       RSQLite_2.4.3         magrittr_2.0.4       
## [16] compiler_4.5.1        rlang_1.1.6           sass_0.4.10          
## [19] tools_4.5.1           yaml_2.3.10           data.table_1.17.8    
## [22] knitr_1.50            labeling_0.4.3        bit_4.6.0            
## [25] curl_7.0.0            diagram_1.6.5         plyr_1.8.9           
## [28] RColorBrewer_1.1-3    withr_3.0.2           purrr_1.1.0          
## [31] RProtoBufLib_2.21.0   BiocGenerics_0.55.1   PeacoQC_1.19.0       
## [34] grid_4.5.1            stats4_4.5.1          flowAI_1.39.0        
## [37] colorspace_2.1-2      scales_1.4.0          iterators_1.0.14     
## [40] tinytex_0.57          dichromat_2.0-0.1     cli_3.6.5            
## [43] rmarkdown_2.30        crayon_1.5.3          ncdfFlow_2.55.0      
## [46] generics_0.1.4        rjson_0.2.23          DBI_1.2.3            
## [49] cachem_1.1.0          flowCore_2.21.0       stringr_1.5.2        
## [52] parallel_4.5.1        BiocManager_1.30.26   matrixStats_1.5.0    
## [55] vctrs_0.6.5           jsonlite_2.0.0        cytolib_2.21.0       
## [58] bookdown_0.45         IRanges_2.43.5        GetoptLong_1.0.5     
## [61] S4Vectors_0.47.4      bit64_4.6.0-1         clue_0.3-66          
## [64] Rgraphviz_2.53.0      magick_2.9.0          foreach_1.5.2        
## [67] jquerylib_0.1.4       hexbin_1.28.5         glue_1.8.0           
## [70] codetools_0.2-20      stringi_1.8.7         gtable_0.3.6         
## [73] shape_1.4.6.1         ggcyto_1.37.1         ComplexHeatmap_2.25.2
## [76] tibble_3.3.0          pillar_1.11.1         rappdirs_0.3.3       
## [79] htmltools_0.5.8.1     graph_1.87.0          circlize_0.4.16      
## [82] R6_2.6.1              dbplyr_2.5.1          httr2_1.2.1          
## [85] doParallel_1.0.17     evaluate_1.0.5        flowWorkspace_4.21.0 
## [88] lattice_0.22-7        Biobase_2.69.1        png_0.1-8            
## [91] memoise_2.0.1         bslib_0.9.0           Rcpp_1.1.0           
## [94] gridExtra_2.3         xfun_0.53             zoo_1.8-14           
## [97] pkgconfig_2.0.3       GlobalOptions_0.1.2