Glimma

Glimma provides interactive visualizations for exploring RNA-sequencing and microarray gene expression analysis results.

Key Features:

• Interactive Graphics: Extends limma plots such as multi-dimensional scaling (MDS) plots and mean-difference (MA) plots with point-level interactivity for querying annotations.
• Enhanced Data Exploration: Reveals per-point annotation and numerical values on demand to inspect dense plots containing tens of thousands of points.
• Plot Linking: Links selections across multiple plots so that highlighted points in one view are reflected in other views.
• Support for Established Workflows: Integrates with Bioconductor workflows based on limma, edgeR, and DESeq2.
• HTML Output: Produces D3/JavaScript-based HTML pages containing the interactive visualizations.
• Reproducibility: Generates consistent, reproducible interactive visualization outputs.

Scientific Applications:

• RNA-sequencing analysis: Exploring gene-level expression, sample relationships, and differential expression results in RNA-seq datasets.
• Microarray gene expression analysis: Inspecting probe- or gene-level differential expression and sample clustering in microarray studies.
• Result interpretation and validation: Supporting hypothesis generation, data validation, and interpretation of differential expression findings.

Methodology:

Extends limma MDS and mean-difference plots with interactive, linked views implemented in D3/JavaScript to produce HTML outputs and integrates with limma, edgeR, and DESeq2.