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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
## 
## 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] ggplot2_3.5.1      reshape2_1.4.4     CytoPipeline_1.5.2 BiocStyle_2.33.1  
## 
## loaded via a namespace (and not attached):
##   [1] changepoint_2.2.4     tidyselect_1.2.1      farver_2.1.2         
##   [4] dplyr_1.1.4           blob_1.2.4            filelock_1.0.3       
##   [7] fastmap_1.2.0         BiocFileCache_2.13.2  XML_3.99-0.17        
##  [10] digest_0.6.37         lifecycle_1.0.4       cluster_2.1.6        
##  [13] RSQLite_2.3.7         magrittr_2.0.3        compiler_4.4.1       
##  [16] rlang_1.1.4           sass_0.4.9            tools_4.4.1          
##  [19] utf8_1.2.4            yaml_2.3.10           data.table_1.16.2    
##  [22] knitr_1.48            labeling_0.4.3        bit_4.5.0            
##  [25] curl_5.2.3            diagram_1.6.5         plyr_1.8.9           
##  [28] RColorBrewer_1.1-3    withr_3.0.1           purrr_1.0.2          
##  [31] RProtoBufLib_2.17.0   BiocGenerics_0.51.3   PeacoQC_1.15.0       
##  [34] grid_4.4.1            stats4_4.4.1          fansi_1.0.6          
##  [37] flowAI_1.35.2         colorspace_2.1-1      scales_1.3.0         
##  [40] iterators_1.0.14      tinytex_0.53          cli_3.6.3            
##  [43] rmarkdown_2.28        crayon_1.5.3          ncdfFlow_2.51.0      
##  [46] generics_0.1.3        httr_1.4.7            rjson_0.2.23         
##  [49] DBI_1.2.3             cachem_1.1.0          flowCore_2.17.0      
##  [52] stringr_1.5.1         zlibbioc_1.51.1       parallel_4.4.1       
##  [55] BiocManager_1.30.25   matrixStats_1.4.1     vctrs_0.6.5          
##  [58] jsonlite_1.8.9        cytolib_2.17.0        bookdown_0.40        
##  [61] IRanges_2.39.2        GetoptLong_1.0.5      S4Vectors_0.43.2     
##  [64] bit64_4.5.2           clue_0.3-65           Rgraphviz_2.49.1     
##  [67] magick_2.8.5          foreach_1.5.2         jquerylib_0.1.4      
##  [70] hexbin_1.28.4         glue_1.8.0            codetools_0.2-20     
##  [73] stringi_1.8.4         gtable_0.3.5          shape_1.4.6.1        
##  [76] ggcyto_1.33.0         ComplexHeatmap_2.21.1 munsell_0.5.1        
##  [79] tibble_3.2.1          pillar_1.9.0          htmltools_0.5.8.1    
##  [82] graph_1.83.0          circlize_0.4.16       R6_2.5.1             
##  [85] dbplyr_2.5.0          doParallel_1.0.17     evaluate_1.0.1       
##  [88] flowWorkspace_4.17.0  lattice_0.22-6        Biobase_2.65.1       
##  [91] highr_0.11            png_0.1-8             memoise_2.0.1        
##  [94] bslib_0.8.0           Rcpp_1.0.13           gridExtra_2.3        
##  [97] xfun_0.48             zoo_1.8-12            pkgconfig_2.0.3      
## [100] GlobalOptions_0.1.2