Last updated: 2025-11-28
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2025_cytoconnect_spatial_workshop/
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Please ensure you follow the instructions below prior to attending the workshop.
Data for all the workshop exercises can be downloaded from Google Drive or Dropbox.
If you have any trouble downloading them, do not worry. We will have a hard copy of the data with us on a thumbdrive that you can copy from on the day of the workshop. Alternatively, we can also AirDrop the files on the day of the workshop.
Create a folder somewhere on your computer (e.g.
C:/2025_cytoconnect_spatial_workshop/ or
/Users/yourname/2025_cytoconnect_spatial_workshop/ ) to
store all the files related for this workhop. Create a data
folder within it and download all the data files into that folder.
Afterwards, under the visium folder, create a new folder
called extdata. We will use this folder to store all the
intermediate analysis files we generate during the workshop.
Your folder structure should look like this:
2025_cytoconnect_spatial_workshop/
└── data
├── imc
│ ├── measurements.csv
│ └── tif_files
│ └── originalimages
│ ├── aSMA.tif
│ ├── Axl.tif
│ ├── CCR6.tif
│ └── ...
│
└── visium
├── extdata
├── spatial
│ ├── aligned_fiducials.jpg
│ ├── aligned_tissue_image.jpg
│ └── ...
├── sc_seurat_object_10x.qs2
├── spots_to_remove_v2.csv
└── Visium_V2_Human_Colon_Cancer_P2_filtered_feature_bc_matrix.h5You need to download the following softwares and install them on your computer prior to the workshop:
After installing R and RStudio, please install the required R packages. You can do this by running the code blocks below in RStudio.
Please install the packages that we will be using in the workshop by running the code block below.
cran_packages <- c(
"Seurat", "ggplot2", "scales", "patchwork", "qs2",
"viridis", "pak", "here", "tidyverse", "uwot", "pheatmap"
)
install.packages(cran_packages)
# RCTD only available on Github
pak::pkg_install("dmcable/spacexr")
bioc_packages <- c()
if(length(bioc_packages) > 0) {BiocManager::install(bioc_packages)}Running this chunk will let you know if the packages have been installed properly.
checkSetup <- function() {
library(cli)
cat("\n--------------------------------------\n")
cat(style_bold(col_magenta("\n***Installing General Packages***\n\n")))
not <- c(); not2 <- c()
packages1 <- c(cran_packages, bioc_packages)#, "Test")
for (i in 1:length(packages1)){
if(requireNamespace(packages1[i], quietly = TRUE)==F) {
cat(paste(style_bold(col_red(packages1[i])), "has not been installed\n"))
not <- c(not,i)
} else {
suppressWarnings(suppressMessages(library(as.character(packages1[i]), character.only = TRUE)))
cat(col_yellow(packages1[i]), "is loaded!\n")
}
}
cat("\n--------------------------------------\n")
if (length(not) > 0){
cat(style_bold(bg_red("\n **IMPORTANT** ")),
style_bold(col_yellow("\n\nYou need to install: \n")),
paste(paste(c(packages1[not]), collapse=", ")),
"\n\n--------------------------------------",
"\n\n Use:\n - install.packages(),\n - BiocManager::install() or, \n - use Google to find installation instructions.\n\n", style_bold(col_green("Then run this function again!\n\n")))
} else {
cat("",col_green(style_bold("\n All packages are loaded!\n\n Happy Coding! :)\n\n")))
}
}
checkSetup()If you have any problems, please reach out to either:
sessionInfo()R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Australia/Perth
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.2
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 httr_1.4.7 cli_3.6.5 knitr_1.50
[5] rlang_1.1.6 xfun_0.53 stringi_1.8.7 processx_3.8.6
[9] promises_1.3.3 jsonlite_2.0.0 glue_1.8.0 rprojroot_2.1.1
[13] git2r_0.36.2 htmltools_0.5.8.1 httpuv_1.6.16 ps_1.9.1
[17] sass_0.4.10 rmarkdown_2.29 jquerylib_0.1.4 tibble_3.3.0
[21] evaluate_1.0.5 fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
[25] whisker_0.4.1 stringr_1.5.2 compiler_4.5.1 fs_1.6.6
[29] pkgconfig_2.0.3 Rcpp_1.1.0 rstudioapi_0.17.1 later_1.4.4
[33] digest_0.6.37 R6_2.6.1 pillar_1.11.0 callr_3.7.6
[37] magrittr_2.0.4 bslib_0.9.0 tools_4.5.1 cachem_1.1.0
[41] getPass_0.2-4
sessionInfo()R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Australia/Perth
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.2
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 httr_1.4.7 cli_3.6.5 knitr_1.50
[5] rlang_1.1.6 xfun_0.53 stringi_1.8.7 processx_3.8.6
[9] promises_1.3.3 jsonlite_2.0.0 glue_1.8.0 rprojroot_2.1.1
[13] git2r_0.36.2 htmltools_0.5.8.1 httpuv_1.6.16 ps_1.9.1
[17] sass_0.4.10 rmarkdown_2.29 jquerylib_0.1.4 tibble_3.3.0
[21] evaluate_1.0.5 fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4
[25] whisker_0.4.1 stringr_1.5.2 compiler_4.5.1 fs_1.6.6
[29] pkgconfig_2.0.3 Rcpp_1.1.0 rstudioapi_0.17.1 later_1.4.4
[33] digest_0.6.37 R6_2.6.1 pillar_1.11.0 callr_3.7.6
[37] magrittr_2.0.4 bslib_0.9.0 tools_4.5.1 cachem_1.1.0
[41] getPass_0.2-4