🗝️🗝️ Conda Env setup code

Seurat4

conda create -n Seurat4
conda activate Seurat4

conda search r-base
conda install -c conda-forge r-base=4.3.2

conda install -c conda-forge r-devtools

# in R
# .libPaths()
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.18")

remotes::install_version(package = 'Seurat', version = package_version('4.4.0'))

install.packages("igraph")
install.packages("RANN")
install.packages("WeightedCluster")
install.packages("corpcor")
install.packages("weights")
install.packages("Hmisc")
install.packages("Matrix")
install.packages("patchwork")
install.packages("plyr")
install.packages("irlba")
if (!requireNamespace("remotes")) install.packages("remotes")
remotes::install_github("GfellerLab/SuperCell")

Giotto

conda create -n Project03 python=3.10
conda activate Project03
conda search r-base
conda install -c conda-forge r-base=4.3.3

conda install conda-forge::r-igraph

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(version = "3.18")

install.packages("igraph")
install.packages("Matrix")
install.packages("survival")


# Seurat v.5
install.packages('Seurat')
setRepositories(ind = 1:3, addURLs = c('https://satijalab.r-universe.dev', 'https://bnprks.r-universe.dev/'))
install.packages(c("BPCells", "presto", "glmGamPoi"))
# Install the remotes package
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
install.packages('Signac')
remotes::install_github("satijalab/seurat-data", quiet = TRUE)
remotes::install_github("satijalab/azimuth", quiet = TRUE)
remotes::install_github("satijalab/seurat-wrappers", quiet = TRUE)

# Giotto
# Necessary for installation from R
if(!"pak" %in% installed.packages()) {
  install.packages("pak")
}
install.packages("colorRamp2")
pak::pak("drieslab/GiottoUtils")

conda install libgdal
conda install conda-forge::geos
conda install conda-forge::proj
conda install -c conda-forge r-terra

pak::pkg_install("drieslab/Giotto")