Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0

Glimma 1.0 introduced intuitive, point-and-click interactive graphics for differential gene expression analysis. Researchers at the Walter and Eliza Hall Institute of Medical Research present a major update to Glimma that brings improved interactivity and reproducibility using high-level visualization frameworks for R and JavaScript. Glimma 2.0 plots are now readily embeddable in R Markdown, thus allowing users to create reproducible reports containing interactive graphics. The revamped multidimensional scaling plot features dashboard-style controls allowing the user to dynamically change the colour, shape and size of sample points according to different experimental conditions. Interactivity was enhanced in the MA-style plot for comparing differences to average expression, which now supports selecting multiple genes, export options to PNG, SVG or CSV formats and includes a new volcano plot function. Feature-rich and user-friendly, Glimma makes exploring data for gene expression analysis more accessible and intuitive.

Schematic diagram for Glimma 2.0

Input data structures from limma, edgeR and DESeq2 RNA-seq analysis workflows are shown on the left, connected to the Glimma functions that accept them. New features for the MDS and summary-expression plots (MA, volcano and XY) are shown in the centre, demarcated by plus signs. Function outputs are listed on the right with several new output formats shown.

Availability –  The stable version of the software is released on Bioconductor and is available at https://bioconductor.org/packages/release/bioc/html/Glimma.html. Both stable and developmental releases of Glimma are available on GitHub at https://github.com/hasaru-k/GlimmaV2.