scFEA: A graph neural network model to estimate cell-wise metabolic using single cell RNA-seq data
github链接GitHub - changwn/scFEA: single cell Flux Estimation Analysis (scFEA) Try the below web server!
seurat对象使用scFEAscFEA/scFEA_tutorial2.ipynb at master · changwn/scFEA · GitHub
1.创建新环境python310
conda create -n python310 python=3.10
2.进入新环境python310
conda activate python310
3.下载scFEA
cd scFEA
conda install --file requirements
conda install pytorch torchvision -c pytorch
pip install --user magic-impute
4.检查scFEA是否安装好
python src/scFEA.py --help
5.尝试运行代码,一直出问题,append的问题
FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
重装了pandas
并将scFEA.py文件第172行改为geneExprDf = pd.concat([geneExprDf, temp], ignore_index=True)
才可以运行