For installation, simply download this repo and run the following commands. Python >= 3.8 is recommended for running copyVAE.
cd copyVAE/
pip install -e .
The following command will run the copy number profiling pipeline.
copyvae path/to/UMI_file path/to/cell_cycle_gene_file
Add flag -g for GPU
Use Macosko_cell_cycle_genes.txt file in data folder for cell cycle gene file.
See Wiki for more details.