GeMSE

GeMSE performs interactive visual analytics of interval-based genomic data and associated metadata to support exploratory analysis of NGS-processed datasets.

Key Features:

• Interactive Analytics: Integrates analysis and visualization to enable on-the-fly cycling among data exploration, analysis, and visualization steps for interval-based genomic data.
• Support for GenoMetric Query Language (GQL): Complements GenoMetric Query Language (GQL) to execute complex queries over heterogeneous processed genomic data.
• Flexible Data Input: Accepts BED, BroadPeak, NarrowPeak, GTF, and general tab-delimited files for numerical features of genomic regions, with metadata as tab-delimited attribute-value text files.
• Explorative Interaction Support: Records past activities to recover results and navigate backward and forward through analysis steps, supporting iterative exploration and comparative visualizations such as heatmaps.
• Practical Use Cases: Demonstrates applications addressing biological questions using heterogeneous genomic datasets.

Scientific Applications:

• NGS exploratory analysis: Supports early-stage interactive exploration and visualization of NGS-processed data to inform analysis decisions.
• Pipeline design and adaptation: Facilitates design and adaptation of NGS data analysis pipelines through iterative visual feedback.
• Query-integrated analyses: Enables integration of complex queries (via GQL) with processed genomic data for cross-dataset analyses.
• Gene expression and regulatory element studies: Applies to analyses ranging from gene expression pattern exploration to identification of regulatory elements.

Methodology:

Implements abstractions that integrate data exploration, analysis, and visualization phases based on principles of interactive analytics and supports iterative workflows for refinement via visual feedback and comparative assessment.