GOseq protocols

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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 1.32.0
Stability Stable
Requirements
AnnotationDbi, stats, graphics, BiocGenerics, utils, rtracklayer, edgeR, R(>=2.11.0), BiasedUrn, GO.db, org.Hs.eg.db, mgcv, geneLenDataBase(>=1.9.2)
Maintained Yes

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  • person_outline Alicia Oshlack <>

Publication for GOseq

GOseq in pipelines

 (181)
2018
PMCID: 5761878
PMID: 29320569
DOI: 10.1371/journal.pone.0190175

[…] (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 [], 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 enrichment […]

2018
PMCID: 5780484
PMID: 29362405
DOI: 10.1038/s41598-018-19950-6

[…] expressed genes from the same two pairwise groups were retained., gene ontology (go) enrichment analysis of differentially expressed genes or lncrna target 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 by differential expressed genes., kegg is a database […]

2018
PMCID: 5785991
PMID: 29374206
DOI: 10.1038/s41598-018-19832-x

[…] with a threshold of fdr ≤ 0.05 and an absolute value of log2ratio ≥ 1 were assigned as differentially expressed. gene ontology functional enrichment analysis of the degs was performed using the goseq r package-based wallenius non-central hyper-geometric distribution., qrt-pcr was carried out to validate the reliability of differentially expressed genes in the lightcycler 480 thermocycler […]

2018
PMCID: 5789592
PMID: 29378511
DOI: 10.1186/s12870-018-1239-z

[…] using the benjamini and hochberg’s approach to control the false discovery rate (fdr). gene ontology (go) enrichment analysis of differentially expressed genes (degs) was implemented with the goseq r software package, in which the gene length bias was corrected. the go terms with degs (fdr ≤ 0.001 and a fold change ≥2) were used for functional enrichment analysis. genes with an adjusted […]

2018
PMCID: 5800670
PMID: 29408927
DOI: 10.1371/journal.pone.0192253

[…] p-value <0.05 and log2 (fold change) ≥1 found by deseq were assigned as differentially expressed., gene ontology (go) enrichment analysis of differentially expressed genes was performed by the goseq r package, in which gene length bias was corrected. go terms with p< 0.05 were considered significantly enriched by differentially expressed genes., kegg provides comprehensive database […]


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GOseq in publications

 (472)
PMCID: 5951829
PMID: 29760381
DOI: 10.1038/s41419-018-0622-x

[…] “complete” method for analyzing different genes based on the same gene ontology (i.e., “regulation of cell proliferation”, “cell cycle” or “aging”) or “hepatocellular carcinoma” marker genes. the goseq r package was used to perform go enrichment analysis of different cluster genes. a corrected p-value < 0.05 was adopted as the standard for judging statistically significant enrichment […]

PMCID: 5948824
PMID: 29751742
DOI: 10.1186/s12864-018-4736-4

[…] we performed kegg pathways analysis using kobas [] application to determine enrichment of these genes in certain pathway. target gene candidates were also subjected to go enrichment analysis. the goseq-based wallenius non-central hyper-geometric distribution [], which adjusts for gene length bias, was used to determine go enrichment significance., to validate the expression of mature mirnas, […]

PMCID: 5946446
PMID: 29747587
DOI: 10.1186/s12864-018-4738-2

[…] 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 [] and used the goseq package [] to estimate enrichment significance via the wallenius approximation method []. we used fdr for multiple testing under dependency [] to adjust p-values. go terms with an fdr < 0.2 […]

PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] considered significant., to explore the function of mrnas, lncrnas and circrnas, the gene ontology (go) and kyoko encyclopedia of genes and genomes (kegg) enrichment analysis were conducted. the goseq (v1.18.0) was used to perform the go enrichment analysis of differentially expressed genes or target genes of lncrnas or source genes of differentially expressed circrnas, in which gene length […]

PMCID: 5946721
PMID: 29719263
DOI: 10.1016/j.celrep.2018.04.004

[…] transcripts were determined by intersecting the top quartiles of three replicates with a cutoff of 50 counts per million aligned reads. gene ontology analysis was performed on the bioconductor goseq package ()., chromatin immunoprecipitation (chip) was performed using 2 μg anti-rna pol ii or 5 μl ctr9 antibody with 25 μg hela chromatin as in . libraries for sequencing were prepared as in , […]


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

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