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clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.

Tianzhi Wu1, Erqiang Hu1, Shuangbin Xu1

  • 1Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.

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PubMed
Summary
This summary is machine-generated.

The updated clusterProfiler 4.0 tool enhances functional enrichment analysis for omics data across thousands of organisms. It offers a universal interface and new features for improved data interpretation and visualization in life sciences.

Keywords:
biological knowledge miningclusterProfilerenrichment analysisfunctional analysisvisualization

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Interpreting high-throughput omics data requires functional enrichment analysis tools.
  • Accurate interpretation relies on up-to-date annotation databases for diverse organisms.
  • Existing tools may lack comprehensive support for multiple species and modern data analysis practices.

Purpose of the Study:

  • To present an updated version of the Bioconductor package, clusterProfiler 4.0.
  • To provide a universal interface for functional enrichment analysis across numerous organisms.
  • To incorporate new features for enhanced data operation, visualization, and analysis.

Main Methods:

  • Updating the clusterProfiler Bioconductor package to version 4.0.
  • Integrating support for thousands of organisms using internal ontologies, pathways, and user-provided/online annotation data.
  • Extending functionalities with tidy interfaces for data operation (dplyr) and visualization (ggplot2).
  • Implementing gene set enrichment analysis and comparative analysis of multiple gene lists.

Main Results:

  • clusterProfiler 4.0 offers a significantly enhanced and universal platform for functional enrichment analysis.
  • The package now supports a vastly expanded range of organisms.
  • New features facilitate tidy data handling, advanced visualization, and comparative analyses of gene sets.
  • The updated version integrates seamlessly with popular data science packages like dplyr and ggplot2.

Conclusions:

  • clusterProfiler 4.0 provides a powerful, versatile, and up-to-date solution for functional enrichment analysis in life sciences.
  • Its broad organismal support and enhanced features make it applicable to diverse omics research scenarios.
  • The package promotes reproducible and efficient interpretation of high-throughput omics data.