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Related Experiment Video

Updated: Jun 24, 2025

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

TOmicsVis: An all-in-one transcriptomic analysis and visualization R package with Shinyapp interface.

Ben-Ben Miao¹, Wei Dong², Zhao-Fang Han¹

¹State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences Xiamen University Xiamen China.

|June 13, 2024

Summary

This summary is machine-generated.

Researchers can now easily analyze and visualize transcriptomic data with TOmicsVis, an R package simplifying complex multigroup experiments. This tool integrates features from multiple R packages for streamlined biological mechanism discovery.

Keywords:

data visualization differential expression enrichment analysis multigroup RNA‐Seq shinyapp

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Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Transcriptomic analysis is crucial for understanding biological mechanisms across species.
Existing R packages for transcriptomics lack unified integration and user-friendly interfaces for complex analyses.

Purpose of the Study:

To develop a comprehensive R package, TOmicsVis (Transcriptomics Visualization), for streamlined transcriptomics data analysis and visualization.
To provide a user-friendly solution integrating features from multiple R packages for multigroup transcriptomic projects.

Main Methods:

Developed TOmicsVis, an R package utilizing 46 other R packages.
Implemented 40 functions covering Sample Statistics, Traits Analysis, Differential Expression, Advanced Analysis, GO and KEGG Enrichment, and Table Operation.
Enabled both local and online (Shiny app) execution for accessibility.

Main Results:

TOmicsVis offers a unified platform for transcriptomics analysis and visualization.
The package streamlines multigroup transcriptomic projects with diverse analytical functions.
Provides accessible tools for researchers with and without coding expertise.

Conclusions:

TOmicsVis enhances the efficiency and accessibility of transcriptomics data analysis.
Facilitates prompt monitoring of experimental data dynamics and rapid exploration of transcriptomics data.
Empowers researchers to uncover biological mechanisms more effectively.