AmpliconRepository Docs

What is AmpliconRepository

AmpliconRepository enables community sharing of focal amplification predictions produced by AmpliconArchitect. It provides a centralized platform to explore, visualize, and download ecDNA and other focal amplification data across thousands of samples.

Key Features: * Unified Search: Find genes, projects, or specific amplicon types (ecDNA, BFB, etc.) with advanced wildcard and logic support. * Co-amplification Analysis: Visualize gene-gene associations and clusters across multiple projects using our interactive graph tool. * Bulk Data Access: Download high-volume sample data in batches, with background processing and email delivery for large requests. * Background Processing: Upload large datasets and manage project versions with automatic background aggregation.

  • Getting Started: Instructions on packaging and uploading your data.
  • Analysis Tools: Detailed guide on using the search, filtering, and graph analysis tools.
  • Download Structure: Description of the schema for project file downloads.
  • FAQ: Common questions and troubleshooting.

Contact & Support

If you have questions, please contact: - Jens Luebeck: jluebeck@ucsd.edu - Ted Liefeld: jliefeld@cloud.ucsd.edu - Vineet Bafna: vbafna@ucsd.edu

or reach out to us on the GitHub issues page.

View the AmpliconSuite GitHub Organization to learn more about the available tools in AmpliconSuite.