GOseq pipeline

GOseq specifications

Information


Unique identifier OMICS_26373
Name GOseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 1.30.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Alicia Oshlack <>

Publication for GOseq

GOseq citations

 (23)
2018
PMCID: 5761878

[…] (fold change)| >1 constituted the threshold to judge the significance of differences in gene expression across libraries. furthermore, go enrichment analysis of the degs was implemented by the goseq r package [32], in which the gene length bias was corrected. in addition, after the data correction with the r package, kobas software (version 2.0.12) was used to test the statistical […]

2018
PMCID: 5816582

[…] 2011; finn et al., 2015), and searched for known annotations within eggnog and go databases (the gene ontology consortium, 2015; huerta-cepas et al., 2016). ontology enrichment was determined using goseq (version 3.4, young et al., 2010), a statistical package for r which accounts for multiple testing as well as differing probe lengths. finally, clustering of gene modules was performed using […]

2018
PMCID: 5821052

[…] nt (ncbi non-redundant nucleotide sequences), ko (kegg ortholog database), go (gene ontology)., gene ontology (go) enrichment analysis of the target genes of die-mirnas was applied using the goseq r packages, which can adjust for gene length biases 29. kegg pathways were determined using the kobas software 30., a total of 24 differentially expressed mirnas, including 15 up-regulated […]

2018
PMCID: 5870212

[…] beijing, china) was used with to identify degs with corrected p-value < 0.05. for further analysis, gene ontology (go) enrichment analysis of differentially expressed genes was implemented by the goseq r package, in which gene length bias was corrected. go terms with corrected p value less than 0.05 were considered significantly enriched among the degs. after getting go enrichment analysis, […]

2018
PMCID: 5946446

[…] tested using the genes expressed in the corresponding sample types (oocytes, innerccs or outerccs) as the background. we obtained go annotations and transcript lengths from biomart [54] and used the goseq package [55] to estimate enrichment significance via the wallenius approximation method [55]. we used fdr for multiple testing under dependency [56] to adjust p-values. go terms with an fdr < […]

GOseq institution(s)
Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, VIC, Australia

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