CellPie

CellPie is a scalable method for spatial transcriptomics factor discovery via joint non-negative matrix factorization.

📄 Preprint available: biorxiv.org

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🚀 Installation

To install CellPie, run the following commands in your terminal:

# Clone the repository
git clone https://github.com/ManchesterBioinference/CellPie  
cd CellPie  

# Create and activate the Conda environment  
conda env create -f environment_cellpie.yml  
conda activate cellpie_env  

# Launch Jupyter Notebook  
jupyter notebook  

⚠️ Important Notice 🚨 Bug Alert: There is a bug in the main_v0 and main_v01 branches, where the W matrix is not updated properly. This issue has been solved in the main branch. So, please only use the main branch instead.