GOstats pipeline

GOstats specifications

Information


Unique identifier OMICS_14555
Name GOstats
Alternative name GO stats
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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Documentation


Maintainer


  • person_outline S. Falcon <>

Publication for GOstats

GOstats citations

 (11)
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 […]

2018
PMCID: 5880070

[…] genes in the adjacency matrix to search for enriched functional annotation. human homologs of these genes were retrieved, and used to evaluate enrichment of the go biological process branch using gostats [39]. to account for the false positives resulting from the multiple testing, we used a false discovery rate (fdr) [40] of ≤35% in holstein and jersey. we used fdr ≤ 60% in brown swiss due […]

2017
PMCID: 5527313

[…] factors was performed using the yeastract database (39). analyses of correlations between data sets and of gene ontology enrichment were performed in r (66) using the base package and the gostats bioconductor package (67). analysis of growth curves obtained from the plate reader experiments was performed in r using the grofit package (68)., microarray data from this study […]

2016
PMCID: 4784345

[…] the fold change of fpkm was computed, and genes with the over or equal to 2-fold change were characterized as degs. functional enrichment analyses were then performed on identified degs by using gostats [29]. for gene ontology and kegg pathway analysis, we used hypergeometric test function (p value < 0.001) [30]., with the rnapure high-purity total rna rapid extraction kit (bioteke), […]

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 […]

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

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