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.Rproj.user/F5A33326/bookdown-crossref/01-HemaScope_installation_tutorial.Rmd.xref
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| h1:installation Installation | ||
| h2:create-a-new-conda-environment-and-activate-it Create a new conda environment and activate it | ||
| h2:set-the-channels-in-conda Set the channels in conda | ||
| h2:install-r-and-python Install R and python | ||
| h2:install-r Install R | ||
| h2:install-required-r-packages Install required R-packages | ||
| h2:create-the-required-python-virtual-environment Create the required python virtual environment | ||
| h2:create-the-required-python-v.3.9.12-virtual-environment Create the required python (v.3.9.12) virtual environment | ||
| h2:the-installed-packages-with-versions The installed packages with versions | ||
|
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| # Installation | ||
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| ## Create a new conda environment and activate it | ||
|
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| ``` | ||
| conda create --name HemaScope_env | ||
| conda activate HemaScope_env | ||
| ``` | ||
|
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| ## Set the channels in conda | ||
|
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| ``` | ||
| # Add the default channel | ||
| conda config --add channels defaults | ||
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| # Add default channel URLs | ||
| conda config --add default_channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main | ||
| conda config --add default_channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/r | ||
| conda config --add default_channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2 | ||
|
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| # Add custom channels | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2 | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/menpo | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch-lts | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/simpleitk | ||
| conda config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/deepmodeling | ||
|
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| # Set to show channel URLs | ||
| conda config --set show_channel_urls true | ||
| ``` | ||
|
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| ## Install R | ||
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| - R 4.3.3 | ||
|
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| ``` | ||
| conda install R-base=4.3.3 | ||
| ``` | ||
|
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| ## Install required R-packages | ||
|
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| - From conda | ||
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| ``` | ||
| conda install -c conda-forge r-devtools=2.4.5 -y | ||
| conda install -c conda-forge r-Seurat=4.3.0.1 -y | ||
| conda install -c conda-forge r-Rfast2=0.1.5.1 -y | ||
| conda install -c conda-forge r-hdf5r=1.3.10 -y | ||
| conda install -c conda-forge r-ggpubr=0.6.0 -y | ||
| conda install pwwang::r-seuratwrappers -y | ||
| conda install -c bioconda bioconductor-monocle=2.28.0 -y | ||
| conda install -c bioconda bioconductor-slingshot=2.8.0 -y | ||
| conda install -c bioconda bioconductor-GSVA=1.48.2 -y | ||
| conda install -c bioconda bioconductor-org.Mm.eg.db=3.17.0 -y | ||
| conda install -c bioconda bioconductor-org.Hs.eg.db=3.17.0 -y | ||
| conda install -c bioconda bioconductor-scran=1.28.1 -y | ||
| conda install -c bioconda bioconductor-AUCell=1.22.0 -y | ||
| conda install -c bioconda bioconductor-RcisTarget=1.20.0 -y | ||
| conda install -c bioconda bioconductor-GENIE3=1.24.0 -y | ||
| conda install -c bioconda bioconductor-biomaRt=2.56.1 -y | ||
| conda install -c bioconda r-velocyto.r=0.6 -y | ||
| #conda install -c bioconda bioconductor-limma=3.56.2 -y | ||
| ``` | ||
| - Enter the R language environment | ||
|
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| We suggest users do not manually update any already installed R packages during the installation of the following R packages. | ||
| ``` | ||
| R | ||
| ``` | ||
| - From BiocManager | ||
|
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||
| ``` | ||
| # BiocManager(version = "1.30.23") should already be installed as a dependency of r-seuratwrappers. | ||
| # If it is not installed, please run the following code to install it. | ||
| # install.packages("BiocManager",version="1.30.23") | ||
| BiocManager::install("ComplexHeatmap") | ||
| BiocManager::install("scmap") | ||
| BiocManager::install("clusterProfiler") | ||
| BiocManager::install("BiocNeighbors") | ||
| ``` | ||
|
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||
| - From CRAN | ||
|
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||
| ``` | ||
| install.packages(c("doMC", | ||
| "doRNG", | ||
| "shinyjs", | ||
| "shiny", | ||
| "shinyWidgets", | ||
| "shinydashboard", | ||
| "slickR", | ||
| "phateR", | ||
| "gelnet", | ||
| "parallelDist", | ||
| "kableExtra", | ||
| "transport", | ||
| "feather", | ||
| "markdown", | ||
| "ggalluvial", | ||
| "forcats", | ||
| "mcmc", | ||
| "MCMCpack", | ||
| "fields", | ||
| "getopt", | ||
| "osfr")) | ||
| ``` | ||
|
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| - From GitHub | ||
|
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| tips: | ||
|
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| Sometimes network connection issues may occur, resulting in an error message indicating that GitHub cannot be connected. Please try installing again when the network conditions improve. | ||
|
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| Usage limitations: Sometimes an API rate limit error occurs, and a GitHub token is needed to provide the GitHub API rate limit. The steps to resolve this are as follows: Register for an account or log in to an existing account on the GitHub website. Then click on your profile picture in the top right corner, go to the dropdown menu and select "Settings." Next, find "Developer settings" and click on it, then find "Personal access tokens (classic)." Click on it, then click "Create new token (classic)." Create a new token by first naming it anything you like. Then choose the expiration time for the token. Finally, check the "repo" box; the token will be used to download code repositories from GitHub. Click "Generate token." Copy the generated token password. | ||
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| After that, set the token in the environment variable in R. Since we are using conda, enter R by typing R in the terminal. Then, enter the command: usethis::edit_r_environ(). This will open a file. Press the i key to edit. Paste the token you copied into the code area as follows: GITHUB_TOKEN="your_token". | ||
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| Then press Esc, type :wq! (force save). After that, you need to exit Linux and re-enter R. Close and reopen the terminal to apply the environment variable. Reopen Linux, activate the conda environment, and enter R again. | ||
|
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| ``` | ||
| devtools::install_github("sqjin/CellChat") | ||
| devtools::install_github("immunogenomics/presto") | ||
| devtools::install_github("aertslab/SCENIC@140ad6b") | ||
| devtools::install_github("pzhulab/abcCellmap@f44c14b") | ||
| devtools::install_github("navinlabcode/copykat@d7d6569") | ||
| devtools::install_github('chris-mcginnis-ucsf/DoubletFinder@8c7f76e') | ||
| devtools::install_github("mojaveazure/seurat-disk@877d4e1") | ||
| devtools::install_github(c("hfang-bristol/dnet")) | ||
|
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| ``` | ||
|
|
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| - Install HemaScopeR from github | ||
|
|
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| ``` | ||
| devtools::install_github(repo="ZhenyiWangTHU/HemaScopeR", dep = FALSE) | ||
| ``` | ||
|
|
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| <!-- - Exist the R language environment --> | ||
| <!-- ``` --> | ||
| <!-- quit() --> | ||
| <!-- ``` --> | ||
|
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| <!-- ## Install required Python-packages --> | ||
|
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| <!-- - Upgrade pip and set mirrors --> | ||
|
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| <!-- ``` --> | ||
| <!-- python -m pip install -i https://pypi.tuna.tsinghua.edu.cn/simple --upgrade pip --> | ||
| <!-- pip config set global.index-url https://pypi.tuna.tsinghua.edu.cn/simple --> | ||
| <!-- pip config set global.extra-index-url http://mirrors.aliyun.com/pypi/simple/ --> | ||
| <!-- ``` --> | ||
|
|
||
| <!-- - Install required packages --> | ||
|
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| <!-- ``` --> | ||
| <!-- pip install anndata arboreto cell2location commot karateclub matplotlib networkx phate pot scanpy scipy scvi-tools seaborn distributed radian dask==2022.2.1 distributed==2022.2.1 scvelo==0.2.5 numpy==1.23.5 pandas==1.5.3 --> | ||
| <!-- # stereopy==1.3.1 --> | ||
| <!-- ``` --> | ||
|
|
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| ## Create the required python (v.3.9.12) virtual environment | ||
|
|
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| - Run the `init_miniconda` function to create the miniconda virtual environments for the scRNA-seq pipeline and ST pipeline of 10X Visium data and MERFISH data. | ||
|
|
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| ``` | ||
| library(HemaScopeR) | ||
| init_miniconda() | ||
| ``` | ||
|
|
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| - (Optional) Run the `init_miniconda_stereo` function to create the miniconda virtual environment for the stereo-seq data. | ||
|
|
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| ``` | ||
| init_miniconda_stereo() | ||
| ``` | ||
|
|
||
|
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||
|
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| ## The installed packages with versions | ||
| - R packages with versions | ||
| ``` | ||
| Package Version | ||
| ------- ------- | ||
|
|
||
| ``` | ||
| - Python packages with versions | ||
| ``` | ||
| Package Version | ||
| ------------------------ -------------- | ||
|
|
||
| ``` |
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