CRAMER

CRAMER visualizes and explores genomic datasets through a customizable genome browser supporting multiple genomic data formats and track-based visualization.

Key Features:

• Multi-Track Genome Visualization: Supports simultaneous visualization of multiple genomic data tracks for parallel exploration of genomic datasets.
• Broad Genomic File Format Support: Accepts genomic data in XML, JSON, BED, VCF, GFF, GFF3, BAM, and delimited text formats.
• Dynamic Track Integration: Enables addition of genomic data tracks from uploaded files or remote FTP repositories with real-time data processing.
• Custom Track Development: Allows creation and modification of visualization tracks using JavaScript.
• Multiple Visualization Instances: Supports simultaneous genome browser instances for comparative examination of different genomic datasets.
• Custom Data Storage: Stores configuration and customization data using a MongoDB database.

Scientific Applications:

• Genomic Data Visualization: Enables visualization of genomic annotations, sequence variants, and sequencing read coverage.
• Variant Analysis: Supports exploration of genomic variation datasets represented in formats such as VCF and BAM.
• Gene Expression and Annotation Studies: Facilitates examination of genomic features and expression-related datasets through track-based genome browsing.

Methodology:

CRAMER processes genomic datasets by loading tracks from supported formats including XML, JSON, BED, VCF, GFF, GFF3, BAM, and delimited files, enabling real-time visualization through a JavaScript-based genome browser deployed on a Node.js server with MongoDB storage.