sevenbridges

sevenbridges provides programmatic API access and an R client for accessing and manipulating genomic data on the Seven Bridges Cancer Genomics Cloud and for integrating Bioconductor packages to support cancer genomics analyses.

Key Features:

• API Integration: Programmatic API interface for accessing and manipulating genomic data stored on the Seven Bridges platform.
• R Client: R client and utilities for issuing API calls and integrating Seven Bridges resources directly within R workflows.
• Interoperability with Bioconductor: Compatibility with Bioconductor and its suite of over 934 packages for bioinformatic and statistical analyses.
• Cancer Genomics Cloud Integration: Integration with the Seven Bridges Cancer Genomics Cloud to access large datasets and computational resources.
• Data management and utilities: Utilities and data management features to support high-throughput genomic and molecular biology research.

Scientific Applications:

• Cancer genomics research: Support for large-scale cancer genomics studies leveraging cloud-hosted datasets and compute.
• Variant calling: Use in workflows for variant calling on large genomic cohorts.
• Gene expression profiling: Support for gene expression profiling analyses within R and Bioconductor ecosystems.
• Pathway analysis: Application to pathway analysis using Bioconductor packages and cloud-accessible data.
• Advanced statistical analysis: Enables application of Bioconductor statistical methods to genomic and molecular datasets.

Methodology:

Programmatic access via an API and an R client with interoperability with Bioconductor; Bioconductor integration relies on community-driven package review processes including formal initial reviews and continuous automated testing.