Single cell resolution spatial technologies like CosMx, Xenium, vizgen and STOmics have moved past the technology demo stages, and are now being applied to real world biological research problems. Many excellent resources cover the preprocessing spatial data from these platforms, and many more package vignettes cover specific tools.

Spatial sampler is instead a collection of How-Tos framed around testing specific biological questions – i.e. comparative tests between experimental conditions.

Each HowTo includes:

Explore these HowTos with the searchable table below.


sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 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_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] dplyr_1.1.4       htmltools_0.5.8.1 reactable_0.4.4   workflowr_1.7.1  

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.9      compiler_4.4.0      BiocManager_1.30.25
 [4] renv_1.0.5          promises_1.3.2      tidyselect_1.2.1   
 [7] Rcpp_1.0.14         stringr_1.5.1       git2r_0.33.0       
[10] callr_3.7.6         later_1.4.1         jquerylib_0.1.4    
[13] yaml_2.3.10         fastmap_1.2.0       R6_2.5.1           
[16] generics_0.1.3      knitr_1.49          htmlwidgets_1.6.4  
[19] tibble_3.2.1        rprojroot_2.0.4     bslib_0.9.0        
[22] pillar_1.10.1       rlang_1.1.5         cachem_1.1.0       
[25] stringi_1.8.4       reactR_0.6.1        httpuv_1.6.15      
[28] xfun_0.50           getPass_0.2-4       fs_1.6.5           
[31] sass_0.4.9          cli_3.6.3           withr_3.0.2        
[34] magrittr_2.0.3      crosstalk_1.2.1     ps_1.8.1           
[37] digest_0.6.37       processx_3.8.5      rstudioapi_0.17.1  
[40] lifecycle_1.0.4     vctrs_0.6.5         evaluate_1.0.3     
[43] glue_1.8.0          whisker_0.4.1       rmarkdown_2.29     
[46] httr_1.4.7          tools_4.4.0         pkgconfig_2.0.3