Here we described a protocol establishing single-cell analysis platform on win10

conda create -n r403py38 python=3.8 numpy matplotlib pandas seaborn
conda activate r403py38 
conda install anaconda-clean 
anaconda-clean --yes conda 
config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/ 

# install compilers 
conda install -c conda-forge llvmlite=0.35 
conda install -c msys2 m2w64-gcc
conda install -c msys2 m2w64-gcc-fortran

# install R 
conda install -c conda-forge r-base=4.0.3

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

# install important r packages
install.packages(c("devtools","Rcpp"))

# install Seurat 4 beta
remotes::install_github("satijalab/seurat", ref = "release/4.0.0")
devtools::install_github('satijalab/seurat-data')
remotes::install_github('satijalab/seurat-wrappers')

# install bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.12")
conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/

BiocManager::install(c('multtest',"SingleCellExperiment","GenomicRanges",
"scRNAseq","Rhdf5lib","pcaMethods","DropletUtils",
"scater","SingleR","geneplotter","AUCell","GSVA",
"M3Drop","ComplexHeatmap","AnnotationHub",
"clusterProfiler","ChIPseeker","ChIPpeakAnno"))

# install monocle
BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats',
'limma', 'S4Vectors', 'SingleCellExperiment',
'SummarizedExperiment', 'batchelor', 'Matrix.utils'))
devtools::install_github('cole-trapnell-lab/leidenbase')
devtools::install_github('cole-trapnell-lab/monocle3')

# install jupyter notebook 
pip install jupyterlab

# install loompy
pip install loompy

pip install scanpy
pip install -i https://mirrors.aliyun.com/pypi/simple python-igraph
pip install -i https://mirrors.aliyun.com/pypi/simple louvain
pip install -i https://mirrors.aliyun.com/pypi/simple leidenalg
pip install -i https://mirrors.aliyun.com/pypi/simple anndata
pip install -i https://mirrors.aliyun.com/pypi/simple scanpy
pip install -i https://mirrors.aliyun.com/pypi/simple -U scvelo

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