Welcome to Spatial Transcriptomic session

‼️ Prerequisite

• Download packages

bio_pkgs = c("BayesSpace","SingleCellExperiment","scran","scater","BiocNeighbors","ComplexHeatmap")
BiocManager::install(bio_pkgs, update = T, force =TRUE)
install.packages("Seurat")
install.packages("ggplot2")
install.packages("dplyr")
install.packages("patchwork")
install.packages("cowplot")
devtools::install_github("sqjin/CellChat")

📙 Documentation for this session can be viewed/downloaded as

• html
  https://parkjooyoung99.github.io/KOGO_2023/KOGO_2023_spatialTranscriptomics_documentation.html

• ppt
  lecture: https://parkjooyoung99.github.io/KOGO_2023/20230131_kogo_srt_jchoi.pdf
  hand-on practice: https://parkjooyoung99.github.io/KOGO_2023/KOGO_2023_spatialTranscriptomics_documentation.pptx

• Rscript
  https://parkjooyoung99.github.io/KOGO_2023/KOGO_2023_spatialTranscriptomics_documentation.R

📗 Reference

• Bayesspace
  https://pubmed.ncbi.nlm.nih.gov/34083791/
  https://edward130603.github.io/BayesSpace/articles/thrane_melanoma.html

• CellChat
  https://pubmed.ncbi.nlm.nih.gov/33597522/
  https://htmlpreview.github.io/?https://github.com/sqjin/CellChat/blob/master/tutorial/CellChat_analysis_of_spatial_imaging_data.html