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EGSEA

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Recognizes differently expressed gene sets in the gene level statistics. EGSEA can assess the association of a set of genes with a phenotype, such as disease or a particular biological process. It is able to simulate a background distribution of an enrichment score by shuffling samples and estimate the statistical significance of a gene set. This tool can determine if a gene set is distinct in some statistically significant way.

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EGSEA classification

  • Animals
    • Homo sapiens
    • Mus musculus
    • Rattus norvegicus

EGSEA specifications

Unique identifier:
OMICS_12476
Alternative name:
GSEA
Interface:
Command line interface
Input data:
Count matrix
Output data:
Significant gene sets
Biological technology:
Illumina
Programming languages:
R
License:
GNU General Public License version 3.0, GNU General Public License version 2.0
Version:
1.6.0
Stability:
Stable
Maintained:
Yes
Name:
Ensemble of Gene Set Enrichment Analyses
Software type:
Package/Module
Restrictions to use:
None
Input format:
R object
Output format:
HTML, csv, png, pdf
Operating system:
Unix/Linux, Mac OS, Windows
Parallelization:
Other
Computer skills:
Advanced
First release date:
2016
Requirements:
Biobase, gage, AnnotationDbi, topGO, pathview

EGSEA distribution

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EGSEA support

Documentation

Maintainers

Credits

Institution(s)

Department of Biostatistics, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Epidemiology, Faculty of Public Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran

Funding source(s)

This work was supported by the AMSI Intern program, NHMRC Project grants (GNT1050661, GNT1045936 and GNT1057854 to MER), a NHMRC Career Development Fellowship (GNT1104924 to MER), Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS.

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