conda create -n scrna0309 python=3.8
conda activate scrna0309
conda install -c conda-forge r-base=3.6.2
pip install scanpy==1.4.6
conda install -c conda-forge r-rcpp
conda install -c conda-forge r-devtools
conda install -c conda-forge leidenalg
pip install loompy
conda install -c conda-forge jupyterlab
conda install -c conda-forge r-hdf5r
pip install -U scvelo
conda install -c conda-forge xorg-libxt
pip install rpy2
git clone https://github.com/aertslab/pySCENIC.git
cd pySCENIC/
pip install .

install.packages('codetools')
install.packages('IRkernel')
IRkernel::installspec(user = T)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.10")
BiocManager::install('multtest')
BiocManager::install("SingleCellExperiment")
BiocManager::install("GenomicRanges")
BiocManager::install("scRNAseq")
BiocManager::install("Rhdf5lib")
BiocManager::install("pcaMethods")
BiocManager::install("DropletUtils") 
BiocManager::install("scater")
install.packages("Matrix")
install.packages("leiden")
install.packages('Seurat')
install.packages("pheatmap")
BiocManager::install("ComplexHeatmap")
BiocManager::install("clusterProfiler")
devtools::install_github('satijalab/seurat-wrappers')
devtools::install_github("constantAmateur/SoupX")
devtools::install_github("velocyto-team/velocyto.R")
BiocManager::install("SingleR") 
BiocManager::install("AUCell")
BiocManager::install("geneplotter")
BiocManager::install("GSVA")
devtools::install_github('MacoskoLab/liger')
BiocManager::install("M3Drop")

wget https://cran.r-project.org/src/contrib/Archive/modes/modes_0.7.0.tar.gz
R CMD INSTALL modes_0.7.0.tar.gz
install.packages("KernSmooth")
install.packages("ROCR")
install.packages("fields")
devtools::install_github('chris-mcginnis-ucsf/DoubletFinder')

conda env create metaseq/scrna0309

pip install scanpy==1.5.1
pip install -U loompy
pip install git+https://github.com/theislab/scvelo
conda install -c conda-forge r-rcpp r-devtools leidenalg r-hdf5r xorg-libxt
BiocManager::install(c('multtest',"SingleCellExperiment","GenomicRanges",
                       "scRNAseq","Rhdf5lib","pcaMethods","DropletUtils",
                       "scater","SingleR","geneplotter","AUCell","GSVA",
                       "M3Drop","ComplexHeatmap","AnnotationHub",
                       "clusterProfiler","ChIPseeker","ChIPpeakAnno"))
devtools::install_github('satijalab/seurat-wrappers') 
devtools::install_github("constantAmateur/SoupX") 
devtools::install_github("velocyto-team/velocyto.R")
devtools::install_github('MacoskoLab/liger')
install.packages(c("Matrix","leiden","pheatmap"))

wget https://cran.r-project.org/src/contrib/Archive/modes/modes_0.7.0.tar.gz 
R CMD INSTALL modes_0.7.0.tar.gz 
install.packages("KernSmooth") 
install.packages("ROCR") 
install.packages("fields") 
devtools::install_github('chris-mcginnis-ucsf/DoubletFinder')