Run the following steps for the atlas integration:
- Highly variable genes search
- Integration with scVI for 36 different hyper-parameter sets
- scIB to compare those 36 models
Create all necessary directories
mkdir -p logs results data
Run highly variable genes search. You will need src, config and data packages installed and accessible to python script
bsub < ./scripts/hvg_script.bsub
Run scvi hyper-parameter search
bsub < ./scripts/run_integration.bsub