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TRNInfer specifications

Information


Unique identifier OMICS_24049
Name TRNInfer
Alternative name Transcriptional Regulatory Networks Infer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Luonan Chen <>
  • person_outline Xiang-Sun Zhang <>

Publication for Transcriptional Regulatory Networks Infer

TRNInfer in publications

 (2)
PMCID: 4412962
PMID: 25937810
DOI: 10.2174/1389202915666141110210634

[…] them into one of them. for instance, reveal also employs mutual information technique beyond boolean network, so it can also belong to correlation-based methods. in (table ), some methods such as trninfer [] and inferelator [] reconstruct the four levels of transcriptional regulatory relationships, while others such as pca-cmi [] and wgcna [] generally identify gene regulations without […]

PMCID: 2823753
PMID: 20047657
DOI: 10.1186/1748-7188-5-1

[…] different levels of sparseness, we applied different thresholds to the connection matrix to get final edges. in our experiments we use murphy's bayesian network toolbox [] for the dbn approach and trninfer[] for the differential equation approach; we refer to them as dbi and dei, respectively., the principle of our phylogenetic approach is that phylogenetically close organisms are likely […]


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TRNInfer institution(s)
School of Information, Renmin University of China, Beijing, China; Academy of Mathematics and Systems Science, CAS, Beijing, China; Institute of Systems Biology, Shanghai University, Shanghai, China; Osaka Sangyo University, Osaka, Japan; ERATO Aihara Complexity Modelling Project, JST, Tokyo, Japan; Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
TRNInfer funding source(s)
Supported by JSPS under JSPS-NSFC collaboration project, the National Nature Science Foundation of China (NSFC) under grant No. 10701080 and the Ministry of Science and Technology, China, under grant No. 2006CB503905.

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