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 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.6.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## 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_1.1.2       CytoPipelineGUI_1.0.0 CytoPipeline_1.2.0   
## [4] BiocStyle_2.30.0     
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.1.3             gridExtra_2.3         rlang_1.1.1          
##   [4] magrittr_2.0.3        clue_0.3-64           GetoptLong_1.0.5     
##   [7] matrixStats_1.0.0     compiler_4.3.1        RSQLite_2.3.1        
##  [10] png_0.1-8             vctrs_0.6.3           reshape2_1.4.4       
##  [13] stringr_1.5.0         pkgconfig_2.0.3       shape_1.4.6          
##  [16] crayon_1.5.2          fastmap_1.1.1         magick_2.7.4         
##  [19] dbplyr_2.3.3          ellipsis_0.3.2        labeling_0.4.2       
##  [22] utf8_1.2.3            promises_1.2.0.1      ncdfFlow_2.48.0      
##  [25] rmarkdown_2.23        graph_1.80.0          purrr_1.0.1          
##  [28] bit_4.0.5             xfun_0.39             zlibbioc_1.48.0      
##  [31] cachem_1.0.8          jsonlite_1.8.7        flowWorkspace_4.14.0 
##  [34] blob_1.2.4            highr_0.10            later_1.3.1          
##  [37] parallel_4.3.1        cluster_2.1.4         R6_2.5.1             
##  [40] bslib_0.5.0           stringi_1.7.12        RColorBrewer_1.1-3   
##  [43] jquerylib_0.1.4       Rcpp_1.0.11           bookdown_0.34        
##  [46] iterators_1.0.14      knitr_1.43            zoo_1.8-12           
##  [49] IRanges_2.36.0        flowCore_2.14.0       httpuv_1.6.11        
##  [52] tidyselect_1.2.0      yaml_2.3.7            doParallel_1.0.17    
##  [55] codetools_0.2-19      curl_5.0.1            lattice_0.21-8       
##  [58] tibble_3.2.1          plyr_1.8.8            Biobase_2.62.0       
##  [61] shiny_1.7.4.1         withr_2.5.0           evaluate_0.21        
##  [64] BiocFileCache_2.10.1  circlize_0.4.15       pillar_1.9.0         
##  [67] BiocManager_1.30.22   filelock_1.0.2        foreach_1.5.2        
##  [70] flowAI_1.32.0         stats4_4.3.1          generics_0.1.3       
##  [73] diagram_1.6.5         S4Vectors_0.40.1      ggplot2_3.4.2        
##  [76] munsell_0.5.0         ggcyto_1.30.0         scales_1.2.1         
##  [79] xtable_1.8-4          PeacoQC_1.12.0        glue_1.6.2           
##  [82] changepoint_2.2.4     tools_4.3.1           hexbin_1.28.3        
##  [85] data.table_1.14.8     XML_3.99-0.14         grid_4.3.1           
##  [88] RProtoBufLib_2.14.0   colorspace_2.1-0      cli_3.6.1            
##  [91] fansi_1.0.4           cytolib_2.14.0        ComplexHeatmap_2.18.0
##  [94] dplyr_1.1.2           Rgraphviz_2.46.0      gtable_0.3.3         
##  [97] sass_0.4.6            digest_0.6.33         BiocGenerics_0.48.0  
## [100] farver_2.1.1          rjson_0.2.21          memoise_2.0.1        
## [103] htmltools_0.5.5       lifecycle_1.0.3       httr_1.4.6           
## [106] GlobalOptions_0.1.2   mime_0.12             bit64_4.0.5