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: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-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] CytoPipeline_1.0.2 BiocStyle_2.28.0  
## 
## loaded via a namespace (and not attached):
##   [1] changepoint_2.2.4     tidyselect_1.2.0      farver_2.1.1         
##   [4] dplyr_1.1.2           blob_1.2.4            filelock_1.0.2       
##   [7] fastmap_1.1.1         BiocFileCache_2.8.0   XML_3.99-0.14        
##  [10] digest_0.6.32         lifecycle_1.0.3       cluster_2.1.4        
##  [13] RSQLite_2.3.1         magrittr_2.0.3        compiler_4.3.1       
##  [16] rlang_1.1.1           sass_0.4.6            tools_4.3.1          
##  [19] utf8_1.2.3            yaml_2.3.7            data.table_1.14.8    
##  [22] knitr_1.43            labeling_0.4.2        bit_4.0.5            
##  [25] curl_5.0.1            diagram_1.6.5         plyr_1.8.8           
##  [28] RColorBrewer_1.1-3    withr_2.5.0           purrr_1.0.1          
##  [31] RProtoBufLib_2.12.0   BiocGenerics_0.46.0   PeacoQC_1.10.0       
##  [34] grid_4.3.1            stats4_4.3.1          fansi_1.0.4          
##  [37] flowAI_1.30.0         colorspace_2.1-0      ggplot2_3.4.2        
##  [40] scales_1.2.1          iterators_1.0.14      cli_3.6.1            
##  [43] rmarkdown_2.23        crayon_1.5.2          ncdfFlow_2.46.0      
##  [46] generics_0.1.3        reshape2_1.4.4        httr_1.4.6           
##  [49] rjson_0.2.21          DBI_1.1.3             cachem_1.0.8         
##  [52] flowCore_2.12.0       stringr_1.5.0         zlibbioc_1.46.0      
##  [55] parallel_4.3.1        BiocManager_1.30.21   matrixStats_1.0.0    
##  [58] vctrs_0.6.3           jsonlite_1.8.7        cytolib_2.12.0       
##  [61] bookdown_0.34         IRanges_2.34.1        GetoptLong_1.0.5     
##  [64] S4Vectors_0.38.1      bit64_4.0.5           clue_0.3-64          
##  [67] Rgraphviz_2.44.0      magick_2.7.4          foreach_1.5.2        
##  [70] jquerylib_0.1.4       hexbin_1.28.3         glue_1.6.2           
##  [73] codetools_0.2-19      stringi_1.7.12        gtable_0.3.3         
##  [76] shape_1.4.6           ggcyto_1.28.0         ComplexHeatmap_2.16.0
##  [79] munsell_0.5.0         tibble_3.2.1          pillar_1.9.0         
##  [82] htmltools_0.5.5       graph_1.78.0          circlize_0.4.15      
##  [85] R6_2.5.1              dbplyr_2.3.2          doParallel_1.0.17    
##  [88] evaluate_0.21         flowWorkspace_4.12.0  lattice_0.21-8       
##  [91] Biobase_2.60.0        highr_0.10            png_0.1-8            
##  [94] memoise_2.0.1         bslib_0.5.0           Rcpp_1.0.10          
##  [97] gridExtra_2.3         xfun_0.39             zoo_1.8-12           
## [100] pkgconfig_2.0.3       GlobalOptions_0.1.2