EGSEA statistics

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Protocols

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 1.8.0
First release date 2016
Stability Stable
Requirements
AnnotationDbi, methods, stats, RColorBrewer, parallel, graphics, Biobase, utils, testthat, BiocStyle, grDevices, knitr, org.Hs.eg.db, org.Mm.eg.db, htmlwidgets, R(>=3.4), ggplot2(>=1.0.0), org.Rn.eg.db, gplots(>=2.14.2), gage(>=2.14.4), topGO(>=2.16.0), pathview(>=1.4.2), PADOG(>=1.6.0), GSVA(>=1.12.0), globaltest(>=5.18.0), limma(>=3.20.9), edgeR(>=3.6.8), HTMLUtils(>=0.1.5), hwriter(>=1.2.2), safe(>=3.4.0), stringi(>=0.5.0), metap, EGSEAdata(>=1.3.1), Glimma(>=1.4.0), plotly, DT
Maintained Yes

Taxon


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

Download


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Versioning


No version available

Documentation


Maintainers


  • person_outline Monther Alhamdoosh
  • person_outline Soheila Khodakarim

EGSEA citations

 (3)
call_split

IFNγ induces PD L1 overexpression by JAK2/STAT1/IRF 1 signaling in EBV positive gastric carcinoma

2017
Sci Rep
PMCID: 5736657
PMID: 29259270
DOI: 10.1038/s41598-017-18132-0
call_split See protocol

[…] GSEA was performed using Bioconductor R packages, including TCGAbiolinks and Ensemble of GSEA (EGSEA),. RNA-sequencing data were downloaded and preprocessed using TCGAbiolinks and annotated with Entrez ID. Differentially expressed genes between EBV (+) and EBV (−) CIN-type GCs were identified u […]

library_books

Easy and efficient ensemble gene set testing with EGSEA

2017
F1000Res
PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] The second dataset analysed in this workflow comes from Lim et al. (2010) and is the microarray equivalent of the RNA-seq data analysed above. Support for microarray data is a new feature in EGSEA, and in this example, we show an express route for analysis according to the steps shown in , from selecting gene sets and building indexes, to configuring EGSEA, testing and reporting the resul […]

library_books

Combining multiple tools outperforms individual methods in gene set enrichment analyses

2016
Bioinformatics
PMCID: 5408797
PMID: 27694195
DOI: 10.1093/bioinformatics/btw623

[…] The performance of the EGSEA method was evaluated using RNA-seq datasets that were either simulated or generated in the course of our research using either human or mouse samples (see Materials and methods section). […]

Citations

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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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