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 4.4.0 alpha (2024-03-27 r86216)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.6.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## locale:
## [1] en_US.UTF-8/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_1.2.0       CytoPipelineGUI_1.2.0 CytoPipeline_1.4.0   
## [4] BiocStyle_2.32.0     
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.2             gridExtra_2.3         rlang_1.1.3          
##   [4] magrittr_2.0.3        clue_0.3-65           GetoptLong_1.0.5     
##   [7] matrixStats_1.2.0     compiler_4.4.0        RSQLite_2.3.5        
##  [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_1.5.2          fastmap_1.1.1         magick_2.8.3         
##  [19] dbplyr_2.5.0          labeling_0.4.3        utf8_1.2.4           
##  [22] promises_1.2.1        ncdfFlow_2.50.0       rmarkdown_2.26       
##  [25] graph_1.82.0          purrr_1.0.2           bit_4.0.5            
##  [28] xfun_0.43             zlibbioc_1.50.0       cachem_1.0.8         
##  [31] jsonlite_1.8.8        flowWorkspace_4.16.0  blob_1.2.4           
##  [34] highr_0.10            later_1.3.2           parallel_4.4.0       
##  [37] cluster_2.1.6         R6_2.5.1              bslib_0.6.2          
##  [40] stringi_1.8.3         RColorBrewer_1.1-3    jquerylib_0.1.4      
##  [43] Rcpp_1.0.12           bookdown_0.38         iterators_1.0.14     
##  [46] knitr_1.45            zoo_1.8-12            IRanges_2.38.0       
##  [49] flowCore_2.16.0       httpuv_1.6.15         tidyselect_1.2.1     
##  [52] yaml_2.3.8            doParallel_1.0.17     codetools_0.2-19     
##  [55] curl_5.2.1            lattice_0.22-6        tibble_3.2.1         
##  [58] plyr_1.8.9            Biobase_2.64.0        shiny_1.8.1          
##  [61] withr_3.0.0           evaluate_0.23         BiocFileCache_2.12.0 
##  [64] circlize_0.4.16       pillar_1.9.0          BiocManager_1.30.22  
##  [67] filelock_1.0.3        foreach_1.5.2         flowAI_1.34.0        
##  [70] stats4_4.4.0          generics_0.1.3        diagram_1.6.5        
##  [73] S4Vectors_0.42.0      ggplot2_3.5.0         munsell_0.5.0        
##  [76] ggcyto_1.32.0         scales_1.3.0          xtable_1.8-4         
##  [79] PeacoQC_1.14.0        glue_1.7.0            changepoint_2.2.4    
##  [82] tools_4.4.0           hexbin_1.28.3         data.table_1.15.4    
##  [85] XML_3.99-0.16.1       grid_4.4.0            RProtoBufLib_2.16.0  
##  [88] colorspace_2.1-0      cli_3.6.2             fansi_1.0.6          
##  [91] cytolib_2.16.0        ComplexHeatmap_2.20.0 dplyr_1.1.4          
##  [94] Rgraphviz_2.48.0      gtable_0.3.4          sass_0.4.9           
##  [97] digest_0.6.35         BiocGenerics_0.50.0   farver_2.1.1         
## [100] rjson_0.2.21          memoise_2.0.1         htmltools_0.5.8      
## [103] lifecycle_1.0.4       httr_1.4.7            GlobalOptions_0.1.2  
## [106] mime_0.12             bit64_4.0.5