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GSEAplot: A Package for Customizing Gene Set Enrichment Analysis in R.

Sarah E Innis1, Kelsie Reinaltt1, Mete Civelek1,2

  • 1Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|April 16, 2021
PubMed
Summary

This study introduces GSEAplot, a new R package that enhances Gene Set Enrichment Analysis (GSEA) with customizable plots and databases. It streamlines genomics analysis by saving results as R objects for easier integration.

Keywords:
R packagefunctional enrichment analysisgene set analysis

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Gene Set Enrichment Analysis (GSEA) identifies biological functions in differentially expressed genes.
  • Existing R implementations lack flexibility, customization, and R object output.

Purpose of the Study:

  • Introduce the GSEAplot R package for enhanced GSEA.
  • Provide novel functionality for analysis and plotting customization.
  • Facilitate GSEA integration into genomics pipelines.

Main Methods:

  • Development of the GSEAplot R package.
  • Implementation of novel functions for saving analysis results as R objects.
  • Addition of customization options for plots and databases.

Main Results:

  • GSEAplot offers flexible analysis and plotting customization.
  • Results are saved as R objects, improving workflow integration.
  • The package provides a novel utility for R-based GSEA in genomics.

Conclusions:

  • GSEAplot enhances GSEA implementation in R.
  • The package improves usability and integration for genomics analysis.
  • It offers a valuable tool for researchers conducting GSEA.