OrthoClust specifications

Information


Unique identifier OMICS_05475
Name OrthoClust
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A network file and a coupling information file.
Input format TSV
Output data A file with three columns: the species id, the gene id given by the input files and a module id.
Output format TSV
Operating system Unix/Linux
Programming languages MATLAB, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Mark Gerstein

Publication for OrthoClust

OrthoClust citations

 (2)
library_books

Expression of immunoproteasome genes is regulated by cell intrinsic and –extrinsic factors in human cancers

2016
Sci Rep
PMCID: 5034284
PMID: 27659694
DOI: 10.1038/srep34019

[…] roups, in order to enrich for gene similarities (same distribution and correlations) between groups during the co-clustering. Both networks and their alignment were fed to the computational framework OrthoClust, which performed co-clustering of all genes. […]

library_books

Enrichment of Triticum aestivum gene annotations using ortholog cliques and gene ontologies in other plants

2015
BMC Genomics
PMCID: 4426649
PMID: 25887590
DOI: 10.1186/s12864-015-1496-2

[…] g, i.e. if a certain GO term exists in 50% or more of the genes in a clique, then it is assigned to the remaining genes in the same clique. A more recent study [], proposes a computational framework (OrthoClust) that integrates single species co-association networks into data clusters across multiple species via orthology relationships. Their framework is applied on RNA-Seq expression profiles of […]

OrthoClust institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA; Department of Genetics, Dartmouth School of Medicine, Hanover, NH, USA
OrthoClust funding source(s)
Supported by the Yale University Faculty of Arts and Sciences High Performance Computing Center.

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