Release v1.0.3

First release of Oncodrive3D, a fast and accurate 3D-clustering algorithm for driver gene discovery. It identifies mutation-enriched volumes by analyzing missense somatic mutations, leveraging AlphaFold's structural predictions to define residue contacts and mutation profiles to simulate neutral mutagenesis. The tool uses rank-based statistics and can process mutations from duplex sequencing studies, enabling the analysis of both cancer and normal tissue datasets across potentially any organism.

Key Updates and Features

Packaging and Linting

• Added Python package build using uv.
• Published the package to PyPI, enabling installation via pip install oncodrive3d.
• Updated the Dockerfile.
• Applied code linting to improve code quality and maintainability.
• Added LICENCE

NextFlow Pipeline Updates

• Restructured the pipeline according to best practices for enhanced performance and maintainability and moved to oncodrive3d_pipeline/.

Documentation Updates

• Updated the README file:
  • Added instructions for installation.
  • Added instructions for running the provided NextFlow pipeline.

Bug Fixes and Refactoring and Others

• Removed preprocessing scripts in build/preprocessing.
• Updated URLs in scripts/datasets/seq_for_mut_prob.py and scripts/plotting/pfam.py to use the January 2024 Ensembl archive.
• Changed output column from Cluster to Clump in the residue-level output (<cohort>.3d_clustering_pos.csv).
• Changed oncodrive3d run input argument from input_maf_path to input_path in scripts/main.py.
• Refactored scripts/datasets/utils.py to improve download functionality and logging.