cbpManager

cbpManager prepares and manages genomic and clinical data for ingestion into cBioPortal for Cancer Genomics.

Key Features:

• Implementation: Implemented as an R package for preparing and managing datasets targeted to cBioPortal for Cancer Genomics.
• Data file generation: Generates, edits, and manages multiple cBioPortal-compatible data files in the specific formats required by cBioPortal.
• Supported data types: Handles mutations, clinical data, patient and sample information, and timeline data.
• Batch processing: Facilitates batch creation and processing of data files for large datasets.
• Modular architecture: Modular framework supports current data types and can be extended to include copy number and fusion data.
• cBioPortal integration: Prepares datasets specifically formatted for ingestion into cBioPortal instances.

Scientific Applications:

• Personalized cancer therapy: Integrates genomic alterations with clinical data to support patient-specific therapeutic decision-making.
• Molecular Tumor Boards and basket studies: Provides formatted datasets to support MTB workflows and genomic-driven basket trial analyses.
• Local cBioPortal instances and data privacy: Enables preparation of datasets for local cBioPortal deployments so patient data can be stored and analyzed within single institutions under privacy constraints.

Methodology:

Generates and edits cBioPortal-formatted data files for mutations, clinical, patient/sample, and timeline data; supports batch processing and uses a modular framework that can be extended to copy number and fusion data.