Demonstration of the CytoPipeline R package suite functionalities

Philippe Hauchamps

Laurent Gatto

Abstract

This vignette provides links to videos demonstrating some of the functionalities of CytoPipeline R package suite. It is distributed, as well as the accompanying videos, under a CC BY-SA license.

Introduction

Background information

Illustrating dataset

Specifying the pipeline

Running the pipeline

Visualizing the results

Comparing pipelines

Example with two different QC methods

Visualizing scale transformations

Defining technical run parameters

Session information

## R Under development (unstable) (2024-02-19 r85946)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.3 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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: UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] BiocStyle_2.31.0
## 
## loaded via a namespace (and not attached):
##  [1] vctrs_0.6.5         cli_3.6.2           knitr_1.45         
##  [4] rlang_1.1.3         xfun_0.42           stringi_1.8.3      
##  [7] purrr_1.0.2         textshaping_0.3.7   jsonlite_1.8.8     
## [10] glue_1.7.0          htmltools_0.5.7     ragg_1.2.7         
## [13] sass_0.4.8          rmarkdown_2.25      evaluate_0.23      
## [16] jquerylib_0.1.4     fastmap_1.1.1       yaml_2.3.8         
## [19] lifecycle_1.0.4     memoise_2.0.1       bookdown_0.37      
## [22] BiocManager_1.30.22 stringr_1.5.1       compiler_4.4.0     
## [25] fs_1.6.3            systemfonts_1.0.5   digest_0.6.34      
## [28] R6_2.5.1            magrittr_2.0.3      bslib_0.6.1        
## [31] tools_4.4.0         pkgdown_2.0.7.9000  cachem_1.0.8       
## [34] desc_1.4.3