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goCluster specifications

Information


Unique identifier OMICS_15648
Name goCluster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.6.0
Stability Stable
Requirements
Biobase
Maintained Yes

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Maintainer


  • person_outline Gunnar Wrobel

Publication for goCluster

goCluster citations

 (4)
library_books

Global transcriptional analysis suggests Lasiodiplodia theobromae pathogenicity factors involved in modulation of grapevine defensive response

2016
BMC Genomics
PMCID: 4981995
PMID: 27514986
DOI: 10.1186/s12864-016-2952-3

[…] (fisher’s exact test, fdr < 0.05) using blast2go software (version 3.0, go-db version 2014–09, []). the goplot package (version 1.0.1, []) in the r environment was used to generate the graph gocluster and gocircle in order to obtain a more detailed view of co-regulated genes in relationship with functional enrichment., to evaluate the capacity of l. theobromae to grow in benzoic acid […]

library_books

How to decide which are the most pertinent overly represented features during gene set enrichment analysis

2007
BMC Bioinformatics
PMCID: 2206060
PMID: 17848190
DOI: 10.1186/1471-2105-8-332

[…] poset (n, ≺)., several methods and tools use a similarity or dissimilarity index to compare sets, we can cite amongst others: funspec [], blastsets [], gostat [], ease [], pandora [], abandapart [], gocluster [], see [] for a review. even though, these methods are using various similarity indices to compare the query and target sets (hypergeometric, binomial, χ2, fisher's exact test, […]

library_books

Mapping biomedical concepts onto the human genome by mining literature on chromosomal aberrations

2007
Nucleic Acids Res
PMCID: 1885641
PMID: 17403693
DOI: 10.1093/nar/gkm054

[…] exact test for finding overrepresented concepts from gene ontology, including fatigo (22), gobar (23), gominer (24), gotoolbox (25), genemerge (26), gotree machine (27), ontologytraverser (28), gocluster (29) and gohypergall in r bioconductor (30)., in blastsets, barriot et al. use the hypergeometric distribution to calculate the probability of having at least the observed number […]

library_books

FACT – a framework for the functional interpretation of high throughput experiments

2005
BMC Bioinformatics
PMCID: 1189078
PMID: 15985174
DOI: 10.1186/1471-2105-6-161

[…] algorithm, which calculates a k-means similarity matrix based on the experimental values and reports on significant terms with the fisher's exact test within the identified groups afterwards (gocluster, g. wrobel, available at ). another analysis module dedicated to the comparison of genomic and expression data runs pairs of two-sided t-tests on the groups of over- and under-expressed […]


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goCluster institution(s)
Biozentrum and Swiss Institute of Bioinformatics, Basel, Switzerland
goCluster funding source(s)
This project is, in part, supported by the Swiss Institute of Bioinformatics.

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