omicsViewer

omicsViewer visualizes ExpressionSet or SummarizedExperiment objects interactively to facilitate data exploration and hypothesis testing.

Key Features:

• Interactive visualization: Features and samples can be selected from data tables or graphs including scatter plots and heatmaps.
• Enrichment analysis: Gene set enrichment analysis is performed on the fly using the Bioconductor package fgsea or Fisher's exact test.
• Network analysis: STRING network analysis is performed dynamically and visualized simultaneously.
• Statistical testing: Significance tests on means (t-test or rank-based test for quantitative phenotype variables) or tests of independence (chi-square or Fisher's exact test for categorical phenotype data) are performed to test associations between phenotype variables and selected samples.
• Modular extensibility: Additional analyses can be added as extra shiny modules.

Scientific Applications:

• Omics data exploration: Interactive exploration of ExpressionSet or SummarizedExperiment objects enables rapid hypothesis generation without requiring R programming knowledge.
• Phenotype association analysis: Statistical testing identifies associations between selected sample subsets and phenotype variables of interest.
• Functional enrichment analysis: On-the-fly enrichment analysis using fgsea or Fisher's exact test identifies enriched gene sets or pathways in selected feature subsets.
• Protein-protein interaction network analysis: STRING network analysis reveals functional relationships among selected features.

Methodology:

The back-end requires preparation of an ExpressionSet with specific header requirements for phenotype data and feature data to ensure front-end recognition while minimizing modification to existing ExpressionSet objects. The front-end is implemented using shiny and plotly.