occdn.limour.top/source/_posts/通过conda安装纯净环境的cellchat.md

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title: 通过conda安装纯净环境的CellChat tags: [] id: '1612' categories:

• - 生信
• • 细胞通讯 date: 2022-03-12 17:52:55 ---

• https://anaconda.org/conda-forge/r-base

• conda create -n cellchat -c conda-forge r-base=4.1.2 -y

• conda activate cellchat

• conda install -c conda-forge r-seurat=4.1.0 -y

• conda install -c conda-forge r-irkernel=1.3 -y

• conda install -c conda-forge r-biocmanager=1.30.16 -y

• conda install -c conda-forge r-devtools=2.4.3 -y

• conda install -c conda-forge r-circlize=0.4.14 -y

• conda install -c conda-forge umap-learn=0.5.3 -y

• conda install -c bioconda bioconductor-biobase=2.54.0 -y

• wget https://github.com/sqjin/CellChat/archive/refs/heads/master.zip -O CellChat-master.zip

• 移除CellChat-master.zip里src目录下的*.so和*.o文件

• unzip CellChat-master.zip

• rm CellChat-master/src/*.so

• rm CellChat-master/src/*.o

• wget https://github.com/jokergoo/ComplexHeatmap/archive/refs/heads/master.zip -O ComplexHeatmap-master.zip

• conda install -c conda-forge r-svglite=2.1.0 -y

• install.packages('NMF')

• devtools::install_local('ComplexHeatmap-master.zip')

• devtools::install_local('CellChat-master')

• IRkernel::installspec(name='cellchat', displayname='r-cellchat')

  Sys.setenv(RETICULATE_PYTHON = "/opt/conda/envs/cellchat/bin/python3.7")
  library('reticulate')
  use_condaenv("cellchat")
  py_config()