Set-up

Working doc: https://docs.google.com/document/d/1JrIMKQEB-9QhlJN9gXKgWbMah5Srl0uA-ZgqqbIiWLY/edit?usp=sharing

Main steps:

1 - Install R and RStudio.

Follow instructions found here to install R and RStudio, which will vary depending on the OS you are using: http://mixomics.org/wp-content/uploads/2016/09/Installation-guide-for-R-and-RStudio.pdf

2 - In RStudio, install the packages listed below.

Install the following R packages through RStudio. Some dependency packages might be required for successful installation. The below packages can be installed by copying the R code into your RStudio console and running. After the package is installed, load it with the function library().

Example:

# ggplot2
install.packages("ggplot2") # install
library("ggplot2") # load

# Install through BiocManager or directly from GitHub with the remotes package.

# BiocManager
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")

BiocManager::install("EBImage")

# SpatialExperiment
BiocManager::install("SpatialExperiment")
# ggspavis
BiocManager::install("ggspavis")
# scater
BiocManager::install("scater")
# scran
BiocManager::install("scran")
# scuttle
BiocManager::install("scuttle")
# DropletUtils
BiocManager::install("DropletUtils")
# nnSVG
BiocManager::install("nnSVG")
# STDeconvolve
BiocManager::install("STdeconvolve")
# LIBD
BiocManager::install("spatialLIBD")


#### CRAN packages

# Enter commands in R (or R studio, if installed)
# Terra
install.packages('terra', repos='https://rspatial.r-universe.dev')
library(terra)
# ggplot2
install.packages("ggplot2")
# Seu
install.packages('Seurat')
library(Seurat)
# Plotly
install.packages("plotly")