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Global and Current Research Trends of Single-Cell Sequencing in Cancer: A Bibliometric and Visualization Study
Published on: April 18, 2025
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Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0
Hasaru Kariyawasam1, Shian Su1, Oliver Voogd1
1Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia.
NAR Genomics and Bioinformatics
|January 6, 2022
Summary
Glimma 2.0 enhances gene expression analysis with interactive, reproducible visualizations. This update improves data exploration and reporting for researchers using R and JavaScript.
Area of Science:
- Bioinformatics
- Computational Biology
- Data Visualization
Background:
- Interactive graphics are crucial for exploring complex biological data.
- Previous versions of Glimma offered basic interactive visualizations for gene expression analysis.
- Reproducibility and enhanced interactivity are key needs in bioinformatics tools.
Purpose of the Study:
- To introduce Glimma 2.0, a major update to the Glimma software.
- To improve the interactivity and reproducibility of differential gene expression analysis visualizations.
- To enable seamless integration of interactive plots into reproducible research reports.
Main Methods:
- Development of Glimma 2.0 using high-level visualization frameworks for R and JavaScript.
- Implementation of embeddable plots for R Markdown documents.
- Revamping multidimensional scaling (MDS) plots with dynamic control options.
- Enhancing MA-style plots with multi-gene selection and export functionalities.
- Introduction of a new volcano plot function.
Main Results:
- Glimma 2.0 plots are now readily embeddable in R Markdown for reproducible reports.
- The updated MDS plot allows dynamic adjustment of sample point aesthetics based on experimental conditions.
- MA-style plots offer enhanced interactivity, including multi-gene selection and various export formats (PNG, SVG, CSV).
- A new volcano plot function has been added for comprehensive data visualization.
Conclusions:
- Glimma 2.0 provides a feature-rich and user-friendly platform for exploring gene expression data.
- The enhanced interactivity and reproducibility empower researchers to conduct more intuitive and accessible data analysis.
- Glimma 2.0 is available on Bioconductor and GitHub, promoting widespread adoption in the scientific community.
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