GOsummaries protocols

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GOsummaries specifications

Information


Unique identifier OMICS_12481
Name GOsummaries
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.16.1
Stability Stable
Requirements
limma, plyr, grid, Rcpp, ggplot2, R(>=2.15), reshape2, gtable, vegan, gProfileR
Maintained Yes

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  • person_outline Raivo Kolde <>

Publication for GOsummaries

GOsummaries in pipelines

 (3)
2015
PMCID: 4541364
PMID: 26286994
DOI: 10.1038/srep13107

[…] were applied for the different cell types. fdr <0.05 was used as threshold in all comparisons., all gene ontology enrichment analyses were performed using the g:profiler web toolkit and r package gosummaries (http://www.bioconductor.org/packages/release/bioc/html/gosummaries.html). to display less redundant and more specific results, gosummaries uses several non-default filtering options […]

2015
PMCID: 4541364
PMID: 26286994
DOI: 10.1038/srep13107

[…] threshold in all comparisons., all gene ontology enrichment analyses were performed using the g:profiler web toolkit and r package gosummaries (http://www.bioconductor.org/packages/release/bioc/html/gosummaries.html). to display less redundant and more specific results, gosummaries uses several non-default filtering options in g:profiler. first, we limited the number of genes in a category; […]

2014
PMCID: 4303946
PMID: 25563934
DOI: 10.1186/1471-2164-15-S12-S5

[…] was carried out in the r package venndiagram []. statistical significance and visualization of gene ontologies for different influences were presented in the form of a "word cloud" in the r package gosummaries []., in addition to the analysis of gene ontologies, the comparisons by kegg and cabio were made to compare the functional characteristics of genes that get activated at different […]


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GOsummaries in publications

 (6)
PMCID: 5478666
PMID: 28634372
DOI: 10.1038/s41598-017-03682-0

[…] the genes annotated to differentially methylated sites and regions, gene ontology and pathway analyses using g:profiler and panther, were carried out, and g:profiler results were aggregated using gosummaries. in site-level analyses, we used the 22,272 differentially methylated cpgs, and the gene ontology analyses were performed separately for 1,464 and 5,196 genes associated with lower […]

PMCID: 4908329
PMID: 27307623
DOI: 10.1093/bioinformatics/btw245

[…] whether the sets of preferentially expressed genes can predict tissue-specific functions, we performed gene ontology (go) enrichment analysis over different sets of tissue-specific markers using gosummaries package in r/bioconductor (). this package uses g:profiler () as backend for enrichment analysis and provides a simple visualization of the results as a word cloud. the coverage […]

PMCID: 4860710
PMID: 27157830
DOI: 10.1038/srep25668

[…] using ipa (ingenuity pathway analysis, quiagen, redwood city, ca) ()., analysis of enriched go terms from the biological process branch was performed separately with the gprofiler webservice via the gosummaries r package for upregulated and downregulated genes for each epilepsy model (). whole genome was used as a reference set. the function ‘gosummaries’ from the gosummaries package was used […]

PMCID: 4541364
PMID: 26286994
DOI: 10.1038/srep13107

[…] were applied for the different cell types. fdr <0.05 was used as threshold in all comparisons., all gene ontology enrichment analyses were performed using the g:profiler web toolkit and r package gosummaries (http://www.bioconductor.org/packages/release/bioc/html/gosummaries.html). to display less redundant and more specific results, gosummaries uses several non-default filtering options […]

PMCID: 4278762
PMID: 25545474
DOI: 10.1371/journal.pone.0115717

[…] to kc and fb)., gene ontology enrichment analysis of differentially expressed genes was performed using g:gost (http://biit.cs.ut.ee/gprofiler/index.cgi) . bases on the p-values of g:gost analysis, gosummaries package were used to generate wordclouds of gene names (http://cran.r-project.org/web/packages/gosummaries/index.html). the word sizes in wordclouds are defined by the p-values., […]


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GOsummaries institution(s)
Institute of Computer Science, University of Tartu, Tartu, Estonia; Quretec, Tartu, Estonia; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
GOsummaries funding source(s)
The research is funded by Estonian Research Council [IUT34-4], target funding [SF0180008s12], ESNATS [HEALTH-F5-2008-201619] and European Regional Development Fund through the EXCS and BioMedIT projects.

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