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Below is a sampler of tests that can be performed on an in-situ single cell spatial datasets. Each example presents just one way of doing things - there are many, many other approaches! These are simply a starting point.

Further information

More information on the source datasets may be found on the data tab.

Initial examples use cosMX data, though approaches should be valid on other platforms like Xenium.

Initial examples use the seurat toolkit, but single feature experiment (bioconductor) examples are in active development.

Session information

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