Contents

1 Demo

(Online version of the book)[https://www.huber.embl.de//msmb]

library("MSMB")
## Loading required package: tibble
dir(system.file("extdata", package = "MSMB"))
##  [1] "01126211_NB8_I025.fcs"  "01247181_NB06_I025.fcs" "02276161_NB8_I025.fcs" 
##  [4] "03157141_NB06_I025.fcs" "05107251_NB06_I025.fcs" "06226101_NB8_I025.fcs" 
##  [7] "07115141_NB8_I025.fcs"  "07215281_NB8_I025.fcs"  "08045071_NB8_I025.fcs" 
## [10] "09225121_NB8_I025.fcs"  "10175181_NB8_I025.fcs"  "10276181_NB8_I025.fcs" 
## [13] "11145351_NB8_I025.fcs"  "12015151_NB8_I025.fcs"  "PaintedTurtles.txt"    
## [16] "annotation.txt"         "statecancerdeaths.csv"
dir(system.file("images", package = "MSMB"))
## [1] "hiv.png"        "image-Cy3.tif"  "image-DAPI.tif" "image-FITC.tif"
## [5] "mosquito.png"
dir(system.file("data", package = "MSMB"))
## [1] "brcalymphnode.RData"  "ukraine_coords.RData" "ukraine_dists.RData"
dir(system.file("scripts", package = "MSMB"))
## [1] "ukraine-dists.R"

2 Session Info

sessionInfo()
## R version 4.5.0 beta (2025-04-02 r88102)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 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] MSMB_1.27.0      tibble_3.2.1     BiocStyle_2.37.0
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37       R6_2.6.1            bookdown_0.43      
##  [4] fastmap_1.2.0       xfun_0.52           magrittr_2.0.3     
##  [7] glue_1.8.0          cachem_1.1.0        knitr_1.50         
## [10] pkgconfig_2.0.3     htmltools_0.5.8.1   rmarkdown_2.29     
## [13] lifecycle_1.0.4     cli_3.6.4           vctrs_0.6.5        
## [16] sass_0.4.10         jquerylib_0.1.4     compiler_4.5.0     
## [19] tools_4.5.0         pillar_1.10.2       evaluate_1.0.3     
## [22] bslib_0.9.0         yaml_2.3.10         BiocManager_1.30.25
## [25] jsonlite_2.0.0      rlang_1.1.6