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OCG specifications

Information


Unique identifier OMICS_11247
Name OCG
Alternative name Overlapping Cluster Generator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained No

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Publication for Overlapping Cluster Generator

OCG in publications

 (9)
PMCID: 5551000
PMID: 28793925
DOI: 10.1186/s40168-017-0307-1

[…] the swissprot protein. as a result, we obtained a human binary interactome containing 74,388 interactions between 12,865 proteins (february 2013)., we detected 855 network modules detected using the overlapping cluster generator algorithm []. modules were functionally annotated by assessing the enrichment of gene ontology (go) biological process and cellular component terms [], and cellular […]

PMCID: 5490940
PMID: 28662117
DOI: 10.1371/journal.pcbi.1005522

[…] sets were calculated to derive a z-influence score so that the background had a mean of 0 and a standard deviation of 1., to analyze topological clusters, the human interactome was submitted to the overlapping cluster generator (ocg) []. slim bp and mf annotations were obtained from go (january 2015)., in the therapy-specific networks, seeds were obtained from drugbank (v3) targets []; […]

PMCID: 5123419
PMID: 28185552
DOI: 10.1186/s12859-016-1191-6

[…] algorithms in chronological order is: mcode [], rnsc [], cfinder [], mcl [], coach [], cmc [], haco [], core [], cfa [], spici [], mcl-caw [], clusterone [], prorank [], the weak ties method [], overlapping cluster generator (ocg) [], plw [], ppsampler2 [], and prorank+ []. further references to existing methods can be found in recent surveys by [, –]., the graph representing a ppin can also […]

PMCID: 4347617
PMID: 25734691
DOI: 10.1186/1471-2105-16-S4-S3

[…] complexes, and hence, it is reasonable to assume that pins have overlapping communities, each containing some multi-functional proteins. few successful hierarchical clustering approaches such as the overlapping cluster generator (ocg) algorithm of [] and the link communities method of [] (to cite just a few) have been recently proposed with the aim of identifying overlapping protein communities […]

PMCID: 4239042
PMID: 25412367
DOI: 10.1371/journal.pone.0112821

[…] requirements or user interpretation. as a result, existing approaches vary to a large degree. methods exist based on clique percolation (cfinder ), local expansion and optimisation (oslom , ocg and clusterone ), agent-based and dynamical algorithms (ganxisw ), approximate minimum degree ordering (mofinder ), normalised cut calculation (graclus ), regularized sparse random graph model […]


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OCG institution(s)
INSERM, U928, TAGC; Université d'Aix-Marseille, France; CNRS, UMR 6206, IML, Marseille, France; CNRS, France
OCG funding source(s)
CNRS (PEPS grant from the STII department of the CNRS); ANR as a Piribio grant (09-PIRI-0028-1, Moonlight project) and as partner of the ERASysBio+ initiative supported under the EU ERA-NET Plus scheme in FP7 (09-SYSB-0008-01 ModHeart project); the AXA Research Fund

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