Usage guidelines

See installation for installation instructions

• Panpipes and the scverse
• General principles for running panpipes
• Panpipes sample submission file
• Using custom genes annotations: gene list formats
• Filtering mudata objects within preprocess pipeline
• Normalization methods
• Running pipeline modules from different entry points.
• Sample submission file for the ingestion of spatial data
• Integration methods implemented in panpipes
• Troubleshooting common issues when running panpipes