# set up env

conda create -n r362 
conda activate r362;

# install R

conda install -c conda-forge r-base

# install analysis-associated packages

install.packages('Rcpp')

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.10")
BiocManager::install('multtest')

install.packages('devtools');
conda install -c conda-forge r-devtools

conda install r-rjava;
conda install -c conda-forge umap-learn
install.packages('Seurat')
devtools::install_github("constantAmateur/SoupX")

conda install -c bioconda scanpy;
RRRRRR
conda install -c conda-forge leidenalg;

# Seurat Ecosystem

BiocManager::install("pcaMethods")
sudo yum install hdf5-devel
conda install -c conda-forge r-hdf5r
devtools::install_github("velocyto-team/velocyto.R")
devtools::install_github('MacoskoLab/liger')
devtools::install_github('satijalab/seurat-wrappers')

install.packages("pheatmap")

# Scanpy Ecosystem

pip install loompy
pip install -U scvelo

# Misc

BiocManager::install("GenomicRanges")
BiocManager::install("SingleCellExperiment")
BiocManager::install("scater")
BiocManager::install("DropletUtils") 
BiocManager::install("SingleR") 
BiocManager::install("scRNAseq")

# install jupyter

conda install -c conda-forge jupyterlab;

install.packages('IRkernel')
IRkernel::installspec(user = FALSE)

# remove env if necessary

conda remove --name r362 --all