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) (2024-01-16 r85808)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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] patchwork_1.2.0       CytoPipelineGUI_1.1.3 CytoPipeline_1.3.6   
## [4] BiocStyle_2.31.0     
## 
## 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_2.4.0          ellipsis_0.3.2        labeling_0.4.3       
##  [22] utf8_1.2.4            promises_1.2.1        ncdfFlow_2.49.0      
##  [25] rmarkdown_2.25        graph_1.81.0          purrr_1.0.2          
##  [28] bit_4.0.5             xfun_0.42             zlibbioc_1.49.0      
##  [31] cachem_1.0.8          jsonlite_1.8.8        flowWorkspace_4.15.4 
##  [34] blob_1.2.4            highr_0.10            later_1.3.2          
##  [37] parallel_4.4.0        cluster_2.1.6         R6_2.5.1             
##  [40] bslib_0.6.1           stringi_1.8.3         RColorBrewer_1.1-3   
##  [43] jquerylib_0.1.4       Rcpp_1.0.12           bookdown_0.37        
##  [46] iterators_1.0.14      knitr_1.45            zoo_1.8-12           
##  [49] IRanges_2.37.1        flowCore_2.15.2       httpuv_1.6.14        
##  [52] tidyselect_1.2.0      yaml_2.3.8            doParallel_1.0.17    
##  [55] codetools_0.2-19      curl_5.2.0            lattice_0.22-5       
##  [58] tibble_3.2.1          plyr_1.8.9            Biobase_2.63.0       
##  [61] shiny_1.8.0           withr_3.0.0           evaluate_0.23        
##  [64] BiocFileCache_2.11.1  circlize_0.4.16       pillar_1.9.0         
##  [67] BiocManager_1.30.22   filelock_1.0.3        foreach_1.5.2        
##  [70] flowAI_1.33.0         stats4_4.4.0          generics_0.1.3       
##  [73] diagram_1.6.5         S4Vectors_0.41.3      ggplot2_3.5.0        
##  [76] munsell_0.5.0         ggcyto_1.31.1         scales_1.3.0         
##  [79] xtable_1.8-4          PeacoQC_1.13.0        glue_1.7.0           
##  [82] changepoint_2.2.4     tools_4.4.0           hexbin_1.28.3        
##  [85] data.table_1.15.0     XML_3.99-0.16.1       grid_4.4.0           
##  [88] RProtoBufLib_2.15.0   colorspace_2.1-0      cli_3.6.2            
##  [91] fansi_1.0.6           cytolib_2.15.2        ComplexHeatmap_2.19.0
##  [94] dplyr_1.1.4           Rgraphviz_2.47.0      gtable_0.3.4         
##  [97] sass_0.4.8            digest_0.6.34         BiocGenerics_0.49.1  
## [100] farver_2.1.1          rjson_0.2.21          memoise_2.0.1        
## [103] htmltools_0.5.7       lifecycle_1.0.4       httr_1.4.7           
## [106] GlobalOptions_0.1.2   mime_0.12             bit64_4.0.5