EGSEA pipeline

EGSEA specifications

Information


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

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

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Documentation


Maintainers


EGSEA IN pipeline

2017
PMCID: 5582413
PMID: 28774883
DOI: 10.15252/emmm.201707565

[…] were carried out with the cufflinks package (trapnell et al, 2012)., gene set enrichment analyses were carried out within the r framework (dobin et al, 2013) using topgo (for geneontology) and egsea (for msigdb) packages., neonatal rat ventricular cardiomyocytes were isolated as previously described (hagenmueller et al, 2010). after plating, nrvcms were allowed to adhere overnight., […]

EGSEA 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
EGSEA 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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