Deep learing-based inferring cell-specific gene regulatory networks from single-cell multiome data
Deep learing-based inferring cell-specific gene regulatory networks from single-cell multiome data
# scMultiomeGRN Deep learing-based inferring cell-specific gene regulatory networks from single-cell multiome data ### Install [MAESTRO](https://github.com/liulab-dfci/MAESTRO)```bashdocker pull winterdongqing/maestro:1.2.1```### Create a conda environment```bash$ conda create -n scMultiomeGRN python bedops meme=5.4.1 perl-bioperl -c bioconda -c conda-forge$ conda activate scMultiomeGRN$ conda install -c bioconda arboreto$ # cpan Parallel::ForkManager$ # cpan Bio::DB::Fasta$ pip install torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu124$ pip install torch_geometric$ pip install lightning h5py pandas scikit-learn scipy tqdm gensim``` ## Runningsee `demo/demo.ipynb`## Citation## ContactJunlin Xu xjl@hnu.edu.cn
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