CellPie is a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization. Preprint is available here https://www.biorxiv.org/content/10.1101/2023.09.29.560213v2
To install CellPie we recommend creating a conda environment using the following commands:
-
Clone the git repo: git clone https://github.com/ManchesterBioinference/CellPie
-
cd into CellPie directory and do: conda env create -f environment.yml
-
conda activate cellpie_env
-
You can load a jupyter notebook by typing 'jupyter notebook' in the command line