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Updated: Jun 30, 2025
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Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
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Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR
Søren Lykke-Andersen1, Jérôme O Rouvière1, Manfred Schmid1
1Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, 8000 Aarhus C, Denmark.
STAR Protocols
|March 19, 2024
Summary
seqNdisplayR is a new R package for visualizing next-generation sequencing data coverage in functional genomics. It offers customizable and reproducible plots, accessible even to R beginners via a Shiny app interface.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Next-generation sequencing (NGS) is crucial for functional genomics.
- Standardized data visualization tools are needed for consistent NGS analysis.
- Existing tools may lack user-friendliness or customization for genomic region visualization.
Purpose of the Study:
- To introduce seqNdisplayR, an R package for visualizing sequencing data coverage.
- To provide a customizable and reproducible method for plotting genomic data.
- To make advanced sequencing data visualization accessible to a wider audience, including R novices.
Main Methods:
- Development of an R package named seqNdisplayR.
- Implementation of a user-friendly "Shiny app" interface for accessibility.
- Detailed documentation on software installation, data preparation, and plotting options.
Main Results:
- seqNdisplayR enables plotting of standard sequencing data coverage within specified genomic regions.
- The package offers customizable and reproducible visualization outputs.
- The Shiny app interface simplifies the process for users without prior R experience.
Conclusions:
- seqNdisplayR provides a valuable tool for functional genomics research.
- The package enhances the standardization and consistency of sequencing data visualization.
- seqNdisplayR promotes broader accessibility to sophisticated bioinformatics tools.
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