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) (2024-11-20 r87352)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## 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] patchwork_1.3.0       CytoPipelineGUI_1.5.0 CytoPipeline_1.7.0   
## [4] BiocStyle_2.35.0     
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3             gridExtra_2.3         rlang_1.1.4          
##   [4] magrittr_2.0.3        clue_0.3-66           GetoptLong_1.0.5     
##   [7] matrixStats_1.4.1     compiler_4.5.0        RSQLite_2.3.8        
##  [10] png_0.1-8             vctrs_0.6.5           reshape2_1.4.4       
##  [13] stringr_1.5.1         pkgconfig_2.0.3       shape_1.4.6.1        
##  [16] crayon_1.5.3          fastmap_1.2.0         magick_2.8.5         
##  [19] dbplyr_2.5.0          labeling_0.4.3        utf8_1.2.4           
##  [22] promises_1.3.0        ncdfFlow_2.53.0       rmarkdown_2.29       
##  [25] graph_1.85.0          tinytex_0.54          purrr_1.0.2          
##  [28] bit_4.5.0             xfun_0.49             zlibbioc_1.53.0      
##  [31] cachem_1.1.0          jsonlite_1.8.9        flowWorkspace_4.19.0 
##  [34] blob_1.2.4            later_1.3.2           parallel_4.5.0       
##  [37] cluster_2.1.6         R6_2.5.1              bslib_0.8.0          
##  [40] stringi_1.8.4         RColorBrewer_1.1-3    jquerylib_0.1.4      
##  [43] Rcpp_1.0.13-1         bookdown_0.41         iterators_1.0.14     
##  [46] knitr_1.49            zoo_1.8-12            IRanges_2.41.1       
##  [49] flowCore_2.19.0       httpuv_1.6.15         tidyselect_1.2.1     
##  [52] yaml_2.3.10           doParallel_1.0.17     codetools_0.2-20     
##  [55] curl_6.0.1            lattice_0.22-6        tibble_3.2.1         
##  [58] plyr_1.8.9            Biobase_2.67.0        shiny_1.9.1          
##  [61] withr_3.0.2           evaluate_1.0.1        BiocFileCache_2.15.0 
##  [64] circlize_0.4.16       pillar_1.9.0          BiocManager_1.30.25  
##  [67] filelock_1.0.3        foreach_1.5.2         flowAI_1.37.0        
##  [70] stats4_4.5.0          generics_0.1.3        diagram_1.6.5        
##  [73] S4Vectors_0.45.2      ggplot2_3.5.1         munsell_0.5.1        
##  [76] ggcyto_1.35.0         scales_1.3.0          xtable_1.8-4         
##  [79] PeacoQC_1.17.0        glue_1.8.0            changepoint_2.3      
##  [82] tools_4.5.0           hexbin_1.28.5         data.table_1.16.2    
##  [85] XML_3.99-0.17         grid_4.5.0            RProtoBufLib_2.19.0  
##  [88] colorspace_2.1-1      cli_3.6.3             fansi_1.0.6          
##  [91] cytolib_2.19.0        ComplexHeatmap_2.23.0 dplyr_1.1.4          
##  [94] Rgraphviz_2.51.0      gtable_0.3.6          sass_0.4.9           
##  [97] digest_0.6.37         BiocGenerics_0.53.3   rjson_0.2.23         
## [100] farver_2.1.2          memoise_2.0.1         htmltools_0.5.8.1    
## [103] lifecycle_1.0.4       httr_1.4.7            GlobalOptions_0.1.2  
## [106] mime_0.12             bit64_4.5.2