install.2021.08

conda install -c conda-forge r-base=4.1.1 r-cairo r-hdf5r libgit2  r-stringi r-curl r-rsqlite r-proj4 r-ggrastr
#conda install -c conda-forge r-cairo r-hdf5r libgit2  r-stringi r-curl r-rsqlite

install.packages(c("tictoc","Rcpp","devtools","tidyverse","ggpubr","Seurat","IRkernel",'pheatmap',"SoupX"))

conda install -y -c anaconda cytoolz
pip install jupyterlab jupyter_contrib_nbextensions jupyter_nbextensions_configurator anndata scanpy scvelo episcanpy pyscenic
jupyter contrib nbextension install --user
jupyter nbextensions_configurator enable --user

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.13")

BiocManager::install(c("limma","multtest",
    "SummarizedExperiment","SingleCellExperiment",
    "GenomicRanges","scRNAseq","Rhdf5lib","DropletUtils","scater","dittoSeq",
    "SingleR","AUCell","GSVA","ComplexHeatmap","AnnotationHub","celldex","EnhancedVolcano",
    "clusterProfiler","ChIPseeker","ChIPpeakAnno","scds"))

devtools::install_git("https://gitee.com/chansigit/liger.git")
devtools::install_git("https://gitee.com/chansigit/seurat-wrappers.git")

# install jupyter notebook R kernel
install.packages('IRkernel')
IRkernel::installspec(user = T)