Article Highlight | 7-Mar-2024

Simplifying complexities in bioinformatics: The advent of OmicsSuite for multi-omics data analysis and visualization

Nanjing Agricultural University The Academy of Science

The revolution in high-throughput sequencing and mass spectrometry technologies, such as Illumina, PacBio, and 10X Genomics, have enabled the production of vast amount of biological data. However, the intricate data formats and the need for specialized analytical pipelines pose significant challenges, especially for experimental biologists who may find command-line interfaces, coding, and scripting daunting.

In September 2023, Horticulture Research published a research entitled by “OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data”.

OmicsSuite is a comprehensive desktop suite that facilitate multi-omics data analysis and visualization, integrating 175 sub-applications across various analysis tasks. Developed with JavaFX for user interaction and R for computational analysis, it supports a wide range of multi-omics studies including plant chloroplast genome analysis, GWAS, transcriptomics, metabolomics, and single-cell RNA-Seq. The key features of OmicsSuite include user-friendly interfaces(UI), comprehensive coverage, highly readable of Multi-omics raw data and output of results through intuitive UI elements.

The OmicsSuite utilizes BioJava for bioinformatics functions and over 300 open-source packages for diverse analytical capabilities. It excels in integrating visualization tools such as ggplot2 and Shiny applications, offering a holistic analysis environment without requiring extensive setup or computational resources. Its architecture enables seamless interaction with the R environment for real-time data processing, supporting vast multi-omics data types from LC-MS data to single-cell genomics formats. OmicsSuite's UI design enhances user experience with modern layout, easy navigation, and comprehensive tutorial support, a computer device with a 4-cores CPU, 4G memory, and 256G storage can perform normal operations of it.

Overall, this toolset simplifies the complex data analysis workflow, making it accessible to researchers in plant breeding and molecular mechanism studies, evidenced by its growing adoption and positive community feedback.




Ben-Ben Miao1, * ,†, Wei Dong2,†, Yi-Xin Gu3, Zhao-Fang Han1, Xuan Luo1, Cai-Huan Ke1 and Wei-Wei You1,4, *

†These authors contributed equally to this work.


1State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, Fujian, China

2Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou 510055,

Guangdong, China

3College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, Guangdong, China

4Fujian Institute for Sustainable Oceans, Xiamen University, Xiamen 361102, Fujian, China

About  Wei-Wei You

Professor of College of Ocean and Earth Sciences, Xiamen University. Vice Dean of Fujian Institute for Sustainable Oceans (Xiamen University). His work focuses on genomics and genetic breeding on shellfish, adaptation mechanism for shellfish aquaculture to multiple climate change stressors, blue food and sustainable aquaculture

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