单细胞转录组相关分析工具安装流程
mamba create -n scanpy conda-forge:scanpy=1.11.5 -y
mamba activate scanpy
mamba install ipykernel -y
# 为了联合使用R
mamba install -c bioconda anndata2ri -y
# 为了聚类
mamba install conda-forge:python-igraph -y
# 为了高变基因
mamba install conda-forge::scikit-misc -y
./miniforge3/bin/conda init
conda activate scanpy
python -m ipykernel install --name scanpy --display-name scanpy
conda deactivate
mamba create -n scvi-tools conda-forge:scvi-tools=1.4.1 conda-forge:scanpy=1.11.5 -y
mamba activate scvi-tools
mamba install ipykernel -y
mamba install conda-forge::scikit-misc -y
mamba install -c conda-forge python-igraph -y
module purge;module load compiler/gcc/9.3.0
pip install scib-metrics
./miniforge3/bin/conda init
conda activate scvi-tools
python -m ipykernel install --name scvi-tools --display-name scvi-tools
conda deactivate
mamba create -n pertpy conda-forge:pertpy=1.0.4 conda-forge:scanpy=1.11.5 python=3.13 -y
mamba activate pertpy
mamba install ipykernel -y
# 为了进行差异分析
pip install 'pertpy[de]'
pip install pydeseq2
# 为了用edger
mamba install conda-forge::rpy2 -y
# 为了使用tcoda
mamba install schrodinger::pyqt6 -y
pip install 'pertpy[tcoda]'
./miniforge3/bin/conda init
conda activate pertpy
python -m ipykernel install --name pertpy --display-name pertpy
conda deactivate
mamba create -n pertpy conda-forge:scanpy=1.11.5 python=3.13 -y
mamba activate pertpy
pip install scikit-misc
pip install pertpy
pip install pydeseq2
mamba create -n scanpro conda-forge:scanpy=1.11.5 -y
mamba activate scanpro
# 细胞比例工具
module purge;module load compiler/gcc/9.3.0 #gcc版本不对导致pip连一些基础的东西都装不上
pip install scanpro
mamba install ipykernel -y
./miniforge3/bin/conda init
conda activate scanpro
python -m ipykernel install --name scanpro --display-name scanpro
conda deactivate
mamba create -n scikit-bio conda-forge:scikit-bio conda-forge:scanpy=1.11.5 -y
mamba activate scikit-bio
mamba install ipykernel -y
./miniforge3/bin/conda init
conda activate scikit-bio
python -m ipykernel install --name scikit-bio --display-name scikit-bio
conda deactivate
mamba create -n cpdb scanpy=1.11.5 -y
mamba activate cpdb
module purge;module load compiler/gcc/9.3.0
pip install cellphonedb
# 下载数据库，注意要解压后其中的cellphonedb.zip才是真正的数据库，不能直接用cellphonedb-data-5.0.0.zip
# https://github.com/ventolab/cellphonedb-data # v5.0.0
# 存储路径：/work/home/acfrxahp1e/software/cpdb/db/v5/cellphonedb.zip
mamba install ipykernel -y
./miniforge3/bin/conda init
conda activate cpdb
python -m ipykernel install --name cpdb --display-name cpdb
conda deactivate
mamba create -n cpdb -c tttpob -c bioconda -c conda-forge cellphonedb=5.0.1 scanpy=1.11.5 -y # Windows下似乎python不能3.14只能3.12
# 下载数据库cellphonedb-data-5.0.0.zip，注意要解压后其中的cellphonedb.zip才是真正的数据库，不能直接用cellphonedb-data-5.0.0.zip
# https://github.com/ventolab/cellphonedb-data # v5.0.0
# 存储路径：D:/System/Documents/GitHub/CellphoneDB/notebooks/data_tutorial/db/v5/cellphonedb.zip
mamba install notebook -c conda-forge -y
mamba install ipykernel -y
mamba create -n celltypist -c bioconda -c conda-forge celltypist scanpy=1.11.5 -y
mamba activate celltypist
# 下载数据库，其实也可以手动下，默认存储在家目录下
python
import celltypist
from celltypist import models
models.download_models()
mamba install ipykernel -y
./miniforge3/bin/conda init
conda activate celltypist
python -m ipykernel install --name celltypist --display-name celltypist
conda deactivate
mamba install pandas -y
mamba install conda-forge::pandoc -y
mamba install bioconda::pysradb -y
# 1. 创建新环境 (Python 3.9 或 3.10 均可)
mamba create -n chatcellanno python=3.9 -y
# 2. 激活环境
conda activate chatcellanno
# 3. 安装必要的轻量级依赖
mamba install pandas pyperclip pyinstaller openpyxl -y
pip install windnd
# (安装 openpyxl 是为了支持未来可能读取 excel，目前 pandas 需要它)
# 4. 确保 tkinter 已安装 (通常 python 自带，如果没有报错则跳过)
python -c "import tkinter; print('Tkinter OK')"
mamba create -n Seurat5 conda-forge::r-seurat=5.4.0 -y
mamba activate Seurat5
mamba install r-irkernel -y
mamba install bioconda::bioconductor-scran -y
./miniforge3/bin/conda init
conda activate Seurat5
R -e "IRkernel::installspec(name = 'Seurat5', displayname = 'Seurat5'"
mamba create -n Monocle3 conda-forge::r-seurat=5.4.0 -y
mamba activate Monocle3
mamba install bioconda::r-monocle3=1.4.26 -y
mamba install r-irkernel -y
./miniforge3/bin/conda init
conda activate Monocle3
R -e "IRkernel::installspec(name = 'Monocle3', displayname = 'Monocle3'"
mamba create -n Clustree conda-forge::r-seurat=5.4.0 -y
mamba activate Clustree
mamba install r-irkernel -y
mamba install -c conda-forge r-tweenr r-systemfonts r-ggforce r-graphlayouts r-backports r-ggraph r-checkmate r-viridis r-tidygraph -y
R
install.packages("clustree") #下载时选18合肥线比较顺利
./miniforge3/bin/conda init
conda activate Clustree
R -e "IRkernel::installspec(name = 'Clustree', displayname = 'Clustree'"
mamba create -n TDEseq r::r-devtools -y
mamba activate TDEseq
mamba install r::r-coneproj -y
mamba install r::r-matrix -y
R
library(devtools)
install_github("Efdix/TDEseq", force=TRUE)
mamba install r-irkernel -y
./miniforge3/bin/conda init
conda activate TDEseq
R
IRkernel::installspec(name='TDEseq', displayname='TDEseq')
quit()
mamba create -n DeepCellSeek
mamba activate DeepCellSeek
mamba install conda-forge::r-devtools -y
mamba install conda-forge::r-tidyverse -y
mamba install -c conda-forge radian -y
mamba install r-irkernel -y
R.exe
devtools::install_github("ZhangLab-Kiz/DeepCellSeek")
quit()
# 为了用notebook，试了下，之后也可以删
mamba install notebook -c conda-forge -y
mamba install r-irkernel -y
mamba create -n r-base conda-forge::r-base=4.5.2 -y
mamba activate r-base
# notebook
mamba install notebook -c conda-forge -y
mamba install r-irkernel -y
mamba install r::r-ggvenndiagram -y
mamba install r::r-patchwork -y
mamba install conda-forge::r-tidyverse -y
mamba install conda-forge::r-eulerr -y
mamba install conda-forge::r-gridextra -y
mamba create -n Enrich conda-forge::r-base=4.5.2 -y
mamba activate Enrich
# notebook
mamba install notebook -c conda-forge -y
mamba install r-irkernel -y
mamba install conda-forge::r-tidyverse -y
R.exe
install.packages("BiocManager")
BiocManager::install("clusterProfiler")
mamba create -n of3_env python=3.10 -y
mamba activate of3_env
mamba install bioconda::orthofinder -y
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.2.0/sratoolkit.3.2.0-centos_linux64.tar.gz #下载3.2.0版，曙光不支持最新版
tar -zxvf sratoolkit.3.2.0-centos_linux64.tar.gz
rm sratoolkit.3.2.0-centos_linux64.tar.gz
export PATH=$PWD/sratoolkit.3.2.0-centos_linux64/bin:$PATH #注意PWD的路径是否正确
mamba install pigz -y
# 在 PowerShell 中运行以下命令，查看当前用户的配置文件路径：
$PROFILE
# 使用文本编辑器（如 VS Code 或 Notepad）打开配置文件：
code $PROFILE # D:\System\Documents\WindowsPowerShell\Microsoft.PowerShell_profile.ps1
# 在配置文件中添加以下内容：
mamba.exe shell hook -s powershell | Out-String | Invoke-Expression
# 保存并关闭配置文件
# 重新启动 PowerShell
jupyter kernelspec list # 查看添加了哪些内核
jupyter kernelspec uninstall xxx -y # 删除xxx内核（注意替换xxx）