setup.md

title	Data & Setup
number-sections	false

::: {.callout-tip level=2}

Workshop Attendees

If you are attending one of our workshops, we will provide a training environment with all of the required software and data.
If you want to setup your own computer to run the analysis demonstrated on this course, you can follow the instructions below. :::

Data

The data used in these materials is provided as a zip file. Download and unzip the folder to your Desktop to follow along with the materials.

Download

Software

• Install R following these instructions

• Open RStudio and run the following command to install the packages used in this course:

  if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
  
  install.packages(c("ggplot2", "dplyr", "pheatmap", "R.utils", "remotes", "paletteer", "devtools", "Rfast2"))
  
  BiocManager::install("Seurat")
  BiocManager::install("SeuratObject")
  BiocManager::install("clusterProfiler")
  BiocManager::install("org.Hs.eg.db")
  BiocManager::install('glmGamPoi')
  BiocManager::install("SpatialExperiment")
  BiocManager::install("SummarizedExperiment")
  BiocManager::install("BiocNeighbors")
  BiocManager::install("ComplexHeatmap")
  
  remotes::install_github('satijalab/seurat-wrappers')
  remotes::install_github("prabhakarlab/Banksy")
  
  devtools::install_github("dmcable/spacexr", build_vignettes = FALSE)
  devtools::install_github('immunogenomics/presto')
  devtools::install_github("jinworks/CellChat")