RamiGO protocols

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Associated diseases

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RamiGO specifications

Information


Unique identifier OMICS_02267
Name RamiGO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.28.0
Stability Stable
Requirements
methods, gsubfn, graph, RCurl, igraph, png
Maintained No

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Documentation


Publication for RamiGO

RamiGO in pipeline

2017
PMCID: 5338265
PMID: 28262816
DOI: 10.1038/srep43923

[…] and lower than 0.8. identified genes with statistically significant changes were categorized according to their function, biological process and cellular component, using the r/bioconductor package ramigo (http://bioconductor.org/packages/release/bioc/html/ramigo.html)., microrna.org (http://www.microrna.org) was used as a resource of microrna target predictions and expression profiles. target […]

RamiGO in publications

 (10)
PMCID: 5757493
PMID: 29379303
DOI: 10.2147/OTT.S154378

[…] www.geneontology.org) and were also mapped to the kegg (www.kegg.jp), which assigns proteins to pathways, to find overrepresented pathways. analyses were done using the software packages gostats and ramigo from bioconductor (www.bioconductor.org). in all cases, p≤0.05 was considered statistically significant., an in silico prediction of which tfs could be regulating multiple genes involved […]

PMCID: 5790494
PMID: 29423077
DOI: 10.18632/oncotarget.23364

[…] among the deregulated functions of the three diseases were evaluated and displayed by venn diagram using the r package ‘venndiagram’ (version 1.6.17)., the go tree were reconstructed by the ‘ramigo’ [], an r package providing functions to interact with the amigo 2 web server (http://amigo2.berkeleybop.org/amigo) and retrieves go trees. to discover the degs for each of es, ccc and ec, […]

PMCID: 5713314
PMID: 29113136
DOI: 10.3390/ijms18112345

[…] method used in this study was set to “pa”, and the correlation matrix rotation method was “promax”. all of the factor elements for each disease were merged together to reconstruct the go tree by “ramigo” [], an r package providing functions to interact with the amigo 2 web server [] and retrieve go trees., the progressive deregulated functions were selected by tracing their rankings […]

PMCID: 5474732
PMID: 28613276
DOI: 10.1038/ncomms15805

[…] to find the most enriched go terms (). significantly enriched go terms (false discovery rate <0.10) were visualized as highlighted boxes within their corresponding go tree depicted by the ramigo r package ()., we used depict for a tissue enrichment analysis to tabulate tissues that are enriched for expression of genes located within ±40 kb of snps with a p<10−5 association […]

PMCID: 5338265
PMID: 28262816
DOI: 10.1038/srep43923

[…] and lower than 0.8. identified genes with statistically significant changes were categorized according to their function, biological process and cellular component, using the r/bioconductor package ramigo (http://bioconductor.org/packages/release/bioc/html/ramigo.html)., microrna.org (http://www.microrna.org) was used as a resource of microrna target predictions and expression profiles. target […]

RamiGO institution(s)
School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland

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