GOstats specifications

Information


Unique identifier OMICS_14555
Name GOstats
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A gene universe and a list of selected genes from that universe
Output data p-value, odds ratio, expected gene count, and actual gene count for each term tested along with the vector of gene identifiers annotated at each term.
Output format HTML
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.40.0
Stability Stable
Requirements Biobase, Category, graph
Maintained Yes

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  • person_outline S. Falcon <>

GOstats article

GOstats citations

 (7)
2018
PMCID: 5796909

[…] the benjamini–hochberg method (41)., differentially expressed genes were analyzed to assess enrichment for kegg, go bp, cc, and mf terms using the conditional hypergeometric test implemented in the gostats r package (function: hypergtest) (42). annotated kegg pathway diagrams were drawn using the pathview r package (43). enrichment of medical subject heading (mesh) terms was evaluated using […]

2016
PMCID: 5035469

[…] were detected using the hclust package in r for hierarchical clustering. genes from individual clusters were submitted to enrichment analysis to identify statistical go term enrichment using the gostats package in r. a reciprocal procedure was also followed in which all genes matching a particular go term were assessed for their combined transcriptional response to infection., initial […]

2016
PMCID: 5308646

[…] based on a hypergeometric test that uses kme [61]., gene ontology (go) enrichment and kyoto encyclopedia of genes and genomes (kegg) pathway analysis of modules was carried out with the r packages gostats and org.hs.eg.db. hypergeometric tests were applied with a p-value cut-off of 0.05 and minimum gene count of 5. each module was tested for go enrichment in terms of the biological process […]

2016
PMCID: 4820810

[…] cells were statistically selected using deseq2 software (|log2fc|>1, fdr<0.05). go terms over-represented in the gene list selected by deseq2 were retrieved by hypergeometric tests using gostats 2.36.0 of r3.2.2 with the annotation packages go.db 3.2.2 and org.mm.eg.db 3.2.3. pathway analysis was performed by hypergeometric tests of differentially expressed genes using keggprofile […]

2016
PMCID: 4734666

[…] using limma with benjamini-hochberg correction for multiple comparisons) and a fold change ≥2. gene ontology (go) overrepresentation analysis (biological processes only) was performed using the gostats bioconductor library in r. the datasets used in this study are deposited in gene expression omnibus (ref: gse68685) in accordance with minimum information about a microarray experiment […]

GOstats institution(s)
Fred Hutchison Cancer Research Center, Program Computational Biology, Seattle, WA, USA

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