EGSEA

The software tool "EGSEA" (Ensemble of Gene Set Enrichment Analyses) addresses the challenge of selecting an optimal gene set enrichment (GSE) analysis method from the increasing number of available tools. Designed for RNA-sequencing data, EGSEA combines results from twelve algorithms, calculating collective gene set scores to enhance the biological relevance of highly ranked gene sets. With a gene set database containing around 25,000 sets from sixteen collections, EGSEA offers multiple visualization capabilities for examining gene sets at various levels of granularity.

Topic

Systems biology

Detail

  • Operation: Gene set testing

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: -

  • Cost: Free

  • Version name: 1.30.0

  • Credit: The AMSI Intern program, NHMRC, NHMRC Career Development Fellowship, Victorian State Government Operational Infrastructure Support and Australian Government.

  • Input: Gene expression matrix [TSV]

  • Output: Data reference [HTML]

  • Contact: Monther Alhamdoosh m.hamdoosh@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • Combining multiple tools outperforms individual methods in gene set enrichment analyses.
  • Alhamdoosh M, et al. Combining multiple tools outperforms individual methods in gene set enrichment analyses. Combining multiple tools outperforms individual methods in gene set enrichment analyses. 2017; 33:414-424. doi: 10.1093/bioinformatics/btw623
  • https://doi.org/10.1093/bioinformatics/btw623
  • PMID: 27694195
  • PMC: PMC5408797

Download and documentation

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