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Information
| Unique identifier | OMICS_17943 |
|---|---|
| Name | GOAtools |
| Alternative name | Gene Ontology Association tools |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | None |
| Input data | GO Association files, NCBI's gene2go GO association file. |
| Input format | GAF |
| Operating system | Unix/Linux |
| Programming languages | Python |
| License | BSD 2-clause “Simplified” License |
| Computer skills | Advanced |
| Version | 0.6.10 |
| Stability | Stable |
| Source code URL | https://codeload.github.com/tanghaibao/goatools/tar.gz/v0.6.10 |
| Maintained | Yes |
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Maintainer
- person_outline Haibao Tang
Publication for Gene Ontology Association tools
GOATOOLS: A Python library for Gene Ontology analyses
GOAtools citations
(34)Molecular mechanisms of fission in echinoderms: Transcriptome analysis
[…] ters were added to the default ones: “-L 25 -N 1 –minins 50 –maxins 600”. A BLAST search against SwissProt database was used for obtaining the GO terms. The GO Enrichment analysis was conducted using GOAtools 0.5.9 [].For finding the unique contigs for fission and norm, we used the number of paired-end reads per contig []. If this number is enough for a 10-fold coverage of contig, the latter is co […]
Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats
[…] e ontology terms, we found significant differences in 74.For each gene ontology group we also tested the enrichment or purification of STRs compared to amount of STRs all the genes in a species using goatools, and correcting for multiple testing with Benjamini-Yekutieli procedure of False Discovery Rate []. […]
Transcriptomic analysis reveals overdominance playing a critical role in nicotine heterosis in Nicotiana tabacum L.
[…] package []. The P-values of DEGs were corrected by Benjamini–Hochberg FDR (false discovery rate) correction []. The over-representation of GO terms and KEGG pathways of DEGs were identified using the Goatools (https://github.com/tanghaibao/Goatools) and R GO package [] respectively. The P-value of the enriched analyses was corrected by the FDR method. […]
Identification of General Patterns of Sex Biased Expression in Daphnia, a Genus with Environmental Sex Determination
[…] nt analysis of GO terms for the 675 core genes with consistent sex-biased expression in all three species, taking the 26’646 genes of D. magna as the reference GO composition. This was done using the GOatools Python script (https://github.com/tanghaibao/goatools), which performs Fisher’s exact tests for differences in frequencies of GO-terms between the two lists (with Bonferroni correction). Enri […]
An Ontology Systems Approach on Human Brain Expression and Metaproteomics
[…] t of linear correlation) to the number of genes found in each taxon to the number of common GO terms found in the same taxon.From all of the GOs obtained, we calculated its semantic similarity by the goatools function semantic_similarity.py. This measure is defined as the reciprocal of the minimal number of branches (or edges) between two GO terms in the GO topology. It can also be defined as the […]
De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust
[…] r each isolate were compared (compare function) and summary heatmaps prepared from the parsed results using ComplexHeatmap (1.12.0) in R. Gene ontology (GO) terms were compared between isolates using goatools and Fisher’s exact test with false-discovery rate and multiple-test correction (https://github.com/tanghaibao/goatools). […]
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