GO-Elite pipeline

GO-Elite specifications

Information


Unique identifier OMICS_26519
Name GO-Elite
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Version 1.2.5
Stability Beta
Source code URL https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/go-elite/GO-Elite_v.1.2.6_dev-Py.zip
Maintained Yes

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Documentation


Maintainer


  • person_outline Nathan Salomonis <>

Additional information


http://code.google.com/p/go-elite/wiki/Tutorials https://code.google.com/archive/p/go-elite/

Publication for GO-Elite

GO-Elite IN pipelines

 (3)
2017
PMCID: 5457141
PMID: 28489004
DOI: 10.7554/eLife.23253.044

[…] et al., 2014). batch effects from library preparation and sequencing were removed using the ruv r package (risso et al., 2014). pathway and functional analysis of gene lists were performed using the go-elite (zambon et al., 2012)., to examine gene expression in arg in human and mouse neocortex, fastq files were obtained using the fastq-dump program of the sra toolkit from the gene expression […]

2016
PMCID: 4913315
PMID: 27321784
DOI: 10.1038/srep28261

[…] component analysis confirmed tight clustering of the control samples (fig. 3b). there was more variability within the trachoma samples, with f11 in particular clustering closer to controls., go-elite software was used to identify a non-redundant set of ontology terms and pathways enriched in stfs17. gene ontology revealed genes associated with extracellular matrix organization, positive […]

2015
PMCID: 4433221
PMID: 25978040
DOI: 10.1371/journal.pone.0124823

[…] final analysis. the normalized raw counts per gene were used to identify genes that were differentially expressed (de) between breeds using edger. gene ontology (go) of de genes was performed using go-elite [22]. classification of functional processes of biological importance and of canonical pathways and networks of de genes were performed using ingenuity systems pathway analysis (ipa; […]

GO-Elite institution(s)
Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA, USA; Department of Bioinformatics-BiGCaT, Maastricht University, Maastricht, The Netherlands; Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA, USA; Departments of Medicine and Molecular and Cellular Pharmacology, University of California, San Francisco, CA, USA
GO-Elite funding source(s)
Supported by grants from the National Institutes of Health (GM080223, GM080223-06S1, HG003053) and the BioRange 1.2.4 research program of the Netherlands Bioinformatics Centre.

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