GenomeGraphs

GenomeGraphs visualizes and integrates diverse genomic datasets and annotations within R to support comparative analysis of array CGH, gene expression, and sequencing data.

Key Features:

• Integrated Visualization: Integrates array CGH, gene expression, sequencing, and other high-throughput experimental datasets into unified genomic plots.
• Dynamic Annotation Queries: Utilizes the biomaRt package to perform live queries to Ensembl databases for gene and transcript annotations.
• Grid Graphics Integration: Leverages the R grid graphics package and viewports to display gene and transcript structures alongside experimental data.
• Custom Annotation Tracks: Supports plotting of user-provided custom annotation tracks aligned to the same genomic coordinate system.
• Extensibility: Extensible within the R environment to accommodate a wide range of genomic datasets.

Scientific Applications:

• Multi-experiment visualization: Combines multiple high-throughput datasets for simultaneous visualization and comparison across genomic regions.
• Sample characterization: Aligns experimental data with gene and transcript annotations to aid interpretation of gene expression patterns.
• Structural variation analysis: Visualizes array CGH and sequencing-derived signals alongside annotations to support identification of structural variants.

Methodology:

Implements plotting in R using grid graphics viewports, performs dynamic Ensembl annotation retrieval via biomaRt, and aligns annotations and experimental tracks on a common genomic coordinate system.