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

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.

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.

Kariyawasam H, Su S, Voogd O, Ritchie ME, Law CW. (2021) Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0. NAR Genomics and Bioinformatics 3(4), lqab116. [article]

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