Spatial transcriptomic analysis codes of erythroblastic islands in mice and humans

R code of spatial transcriptomic data analysis The xenium analysis codes were run with R (version 4.3.3) and RStudio (2023.12.1) using Mac Pro (Apple M2 Ultra chip, macOS Sonoma 14.5 and 192 GB memory). Giotto Suite (version 4.0.5) package was used for the analysis. The visium analysis codes were run with R (version 4.3.2) and RStudio (2023.09.1) using MacBook Pro (Apple M1 chip, macOS Sonoma 14.3.1 and 8 GB memory). Giotto Suite (version 4.0.2) package was used for the analysis. The single cell RNA seq analysis codes were run with R (version 4.3.3) and RStudio (2023.12.1) using Mac Pro (Apple M2 Ultra chip, macOS Sonoma 14.5 and 192 GB memory). Giotto Suite (version 4.0.5) and Seurat (version 5.0.3) packages were used for the analysis. Instructions for R and RStudio installation can be found with the link: https://rstudio-education.github.io/hopr/starting.html, and Giotto Suite and Seurat packages can be installed according to the guides of these websites: https://drieslab.github.io/Giotto_website/articles/installation.html and https://satijalab.org/seurat/articles/install_v5 All the installation could be finished in two hours on a normal desktop computer. For the analysis, be access and download these datasets from GEO database. Open RStudio, and import individual code into RStudio and run it step by step for individual dataset analysis.