0. Create initial clean R environment

module load anaconda

conda create -n r-environment r-essentials r-base r-biocmanager r-devtools

conda activate r-environment

conda install -c conda-forge r-rsvg
conda install -c conda-forge r-magick
conda install -c bioconda bioconductor-jaspar2020
conda install -c conda-forge r-locfit
conda install -c conda-forge r-ggalluvial
conda install -c bioconda bioconductor-scran
conda install -c conda-forge r-forcats
conda install -c conda-forge r-rgeos
conda install -c conda-forge r-seurat
conda install -c bioconda bioconductor-rsamtools
conda install -c bioconda r-monocle3
conda install -c bioconda bioconductor-dirichletmultinomial

conda env export > environment.yml

1a. Create virtual R environment

export PROJECT_DIR="$HOME/R_analysis/"

cd $PROJECT_DIR
R
install.packages("renv")
renv::init(project="sc_kidney")
q()

cd sc_kidney/

1b. Install required packages

R
renv::install("evaluate", rebuild=TRUE)
renv::install("cli", rebuild=TRUE)
renv::install("sessioninfo", rebuild=TRUE)
renv::install("devtools", rebuild=TRUE)
renv::install("bitops", rebuild=TRUE)
renv::install("RCurl", rebuild=TRUE)
renv::install("parallelly", rebuild=TRUE)
renv::install("BiocManager", rebuild=TRUE)
renv::install("bioc::S4Vectors")
renv::install("bioc::IRanges")
renv::install("bioc::GenomeInfoDb")
renv::install("bioc::XVector")
renv::install("bioc::GenomicRanges")
renv::install("bioc::Biobase")
renv::install("bioc::lattice")
renv::install("bioc::Matrix")
renv::install("bioc::SummarizedExperiment")
renv::install("bioc::Rhtslib")
renv::install("bioc::Biostrings")
renv::install("bioc::Rsamtools")
renv::install("bioc::GenomicAlignments")
renv::install("bioc::XML")
renv::install("bioc::rtracklayer")
renv::install("bioc::codetools")
renv::install("bioc::KEGGREST")
renv::install("bioc::rlang")
renv::install("bioc::digest")
renv::install("bioc::Rcpp")
renv::install("bioc::magrittr")
renv::install("bioc::mime")
renv::install("bioc::ellipsis")
renv::install("bioc::fastmap")
renv::install("bioc::shiny")
renv::install("blob")
renv::install("RSQLite")
renv::install("vctrs")
renv::install("cachem")
renv::install("stringr")
renv::install("data.table")
renv::install("tidyr")
renv::install("bioc::AnnotationDbi")
renv::install("bioc::annotate")
renv::install("bioc::Rtsne")
renv::install("bioc::fansi")
renv::install("bioc::utf8")
renv::install("bioc::tibble")
renv::install("stringi")
renv::install("bioc::CNEr")
renv::install("bioc::matrixStats")
renv::install("bioc::BSgenome")
renv::install("bioc::BSgenome.Mmusculus.UCSC.mm10")
renv::install("bioc::TFBSTools")
renv::install("bioc::chromVAR")
renv::install("bioc::motifmatchr")
renv::install("bioc::universalmotif")
renv::install("readxl")
renv::install("dplyr")
renv::install("rsvg")
renv::install("gapminder")
renv::install("pheatmap")
renv::install("kit")
renv::install("svglite")
renv::install("ggnewscale")
devtools::install_github("GreenleafLab/ArchR", ref="master",
                         repos = BiocManager::repositories())
library(ArchR)
ArchR::installExtraPackages()
devtools::install_github("GreenleafLab/chromVARmotifs")
renv::install("hexbin")