GeneTonic

GeneTonic interprets and integrates results from differential expression analysis and functional enrichment analysis of RNA-sequencing datasets to generate insightful observations and hypotheses.

Key Features:

• Interactive Exploration: Provides interactive widgets that link core elements together for efficient drill-down tasks at increasing levels of detail.
• Reproducible Reporting: Captures features and gene sets of interest highlighted during live sessions and creates an HTML report where text, code, and output coexist.
• Standardized Data Container: Uses the GeneTonicList as a standardized container for all required components to simplify generation of multiple visualizations and summaries.
• Integration with Bioconductor: Maintains interoperability with essential classes and gold-standard pipelines implemented in the open-source Bioconductor project.

Scientific Applications:

• RNA-seq Data Interpretation: Contextualizes and integrates differential expression results with functional enrichment analyses for transcriptome profiling experiments.
• Functional Enrichment Analysis: Combines transcriptome data and results from functional enrichment analysis to facilitate hypothesis generation.
• Downstream Differential Expression Analysis: Extracts information quickly and effectively downstream of the differential expression step.

Methodology:

GeneTonic accepts a GeneTonicList as a standardized container for all required components and generates visualizations and summaries from combined differential expression and functional enrichment results.