MicroScope

MicroScope visualizes and analyzes genomic datasets from ChIP-seq and RNA-seq to provide integrated, multi-layered insights into gene regulation and expression.

Key Features:

• Interactive Visualization: Interactive heatmaps depict genomic activity across ChIP-seq and RNA-seq next-generation sequencing datasets to enable dynamic exploration of signals.
• Multi-scale Insight: Integrates differential expression analysis, principal component analysis (PCA), gene ontology analysis, and dynamic network analysis to provide layered interpretation of genomic data.
• Comprehensive Analysis Tools: Implements differential expression analysis to identify genes with significant changes between conditions, PCA for dimensionality reduction and pattern detection, gene ontology analysis for functional annotation, and dynamic network analysis to explore interactions within genomic networks.

Scientific Applications:

• Regulatory element identification: Supports analysis of ChIP-seq data to identify key regulatory elements and protein–DNA interaction sites.
• Gene expression profiling: Supports RNA-seq differential expression analysis to characterize gene expression patterns across conditions.
• Network and epigenetic analysis: Enables exploration of dynamic genomic networks and epigenetic patterns relevant to genomics, transcriptomics, and epigenetics.

Methodology:

Implemented in R with integration of the D3 JavaScript library for visualization; methods explicitly include interactive heatmap generation, differential expression analysis, principal component analysis (PCA), gene ontology analysis, and dynamic network analysis.