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 Under development (unstable) (2025-11-04 r88984)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.8
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] ggplot2_4.0.1       reshape2_1.4.5      CytoPipeline_1.11.1
## [4] BiocStyle_2.39.0   
## 
## 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_1.3.0            filelock_1.0.3       
##  [7] S7_0.2.1              fastmap_1.2.0         BiocFileCache_3.1.0  
## [10] XML_3.99-0.20         digest_0.6.39         lifecycle_1.0.5      
## [13] cluster_2.1.8.1       RSQLite_2.4.5         magrittr_2.0.4       
## [16] compiler_4.6.0        rlang_1.1.6           sass_0.4.10          
## [19] tools_4.6.0           yaml_2.3.12           data.table_1.17.8    
## [22] knitr_1.51            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_1.2.1          
## [31] RProtoBufLib_2.23.0   BiocGenerics_0.57.0   PeacoQC_1.21.0       
## [34] grid_4.6.0            stats4_4.6.0          flowAI_1.41.0        
## [37] colorspace_2.1-2      scales_1.4.0          iterators_1.0.14     
## [40] tinytex_0.58          dichromat_2.0-0.1     cli_3.6.5            
## [43] rmarkdown_2.30        crayon_1.5.3          ncdfFlow_2.57.0      
## [46] generics_0.1.4        otel_0.2.0            rjson_0.2.23         
## [49] DBI_1.2.3             cachem_1.1.0          flowCore_2.23.1      
## [52] stringr_1.6.0         parallel_4.6.0        BiocManager_1.30.27  
## [55] matrixStats_1.5.0     vctrs_0.6.5           jsonlite_2.0.0       
## [58] cytolib_2.23.0        bookdown_0.46         IRanges_2.45.0       
## [61] GetoptLong_1.1.0      S4Vectors_0.49.0      bit64_4.6.0-1        
## [64] clue_0.3-66           Rgraphviz_2.55.0      magick_2.9.0         
## [67] foreach_1.5.2         jquerylib_0.1.4       hexbin_1.28.5        
## [70] glue_1.8.0            codetools_0.2-20      stringi_1.8.7        
## [73] gtable_0.3.6          shape_1.4.6.1         ggcyto_1.39.1        
## [76] ComplexHeatmap_2.27.0 tibble_3.3.1          pillar_1.11.1        
## [79] rappdirs_0.3.3        htmltools_0.5.9       graph_1.89.1         
## [82] circlize_0.4.17       R6_2.6.1              dbplyr_2.5.1         
## [85] httr2_1.2.2           doParallel_1.0.17     evaluate_1.0.5       
## [88] flowWorkspace_4.23.1  lattice_0.22-7        Biobase_2.71.0       
## [91] png_0.1-8             memoise_2.0.1         bslib_0.9.0          
## [94] Rcpp_1.1.1            gridExtra_2.3         xfun_0.55            
## [97] zoo_1.8-15            pkgconfig_2.0.3       GlobalOptions_0.1.3