GOAtools statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GOAtools
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Tool usage distribution map

This map represents all the scientific publications referring to GOAtools per scientific context
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Associated diseases

This word cloud represents GOAtools usage per disease context
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Protocols

GOAtools specifications

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 citations

 (34)
library_books

Molecular mechanisms of fission in echinoderms: Transcriptome analysis

2018
PLoS One
PMCID: 5897022
PMID: 29649336
DOI: 10.1371/journal.pone.0195836

[…] 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 […]

library_books

Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats

2018
BMC Genomics
PMCID: 5894186
PMID: 29636006
DOI: 10.1186/s12864-018-4616-y

[…] 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 []. […]

library_books

Transcriptomic analysis reveals overdominance playing a critical role in nicotine heterosis in Nicotiana tabacum L.

2018
BMC Plant Biol
PMCID: 5863848
PMID: 29566653
DOI: 10.1186/s12870-018-1257-x

[…] 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. […]

library_books

Identification of General Patterns of Sex Biased Expression in Daphnia, a Genus with Environmental Sex Determination

2018
PMCID: 5940145
PMID: 29535148
DOI: 10.1534/g3.118.200174

[…] 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 […]

library_books

An Ontology Systems Approach on Human Brain Expression and Metaproteomics

2018
Front Microbiol
PMCID: 5852110
PMID: 29568289
DOI: 10.3389/fmicb.2018.00406

[…] 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 […]

library_books

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

2018
MBio
PMCID: 5821079
PMID: 29463655
DOI: 10.1128/mBio.01650-17

[…] 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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GOAtools institution(s)
School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, PA, USA; Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China; Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Department of Genetics, Evolution and Environment, University College London, London, UK; Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; UC Berkeley - UCSF Graduate Program in Bioengineering, University of California, San Francisco, CA, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, CA, USA; Independent Researcher, Philadelphia, PA, USA; Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
GOAtools funding source(s)
Supported by the Fujian provincial government for a Fujian “100 Talent Plan” award.

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