TimeDelay-ARACNE statistics

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TimeDelay-ARACNE specifications

Information


Unique identifier OMICS_10586
Name TimeDelay-ARACNE
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 1.30.0
Stability Stable
Requirements
Biobase, Rgraphviz, GenKern
Maintained Yes

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Documentation


Maintainer


  • person_outline Michele Ceccarelli <>

Publication for TimeDelay-ARACNE

TimeDelay-ARACNE in publications

 (7)
PMCID: 5294223
PMID: 28243601
DOI: 10.1155/2017/6261802

[…] were implemented in the r programming language using steady state data [] and time-series data []. the tool using steady state data is named aracne [] and the tool using time-series data is named timedelay-aracne []. aracne infers an undirected network, which basically shows whether two genes are mutually dependent rather than the regulatory relationship between the genes. in contrast, […]

PMCID: 5104482
PMID: 27832153
DOI: 10.1371/journal.pone.0166084

[…] the context likelihood of relatedness (clr) algorithm, also used mutual information as a metric of similarity between the expression profiles of two genes. zoppoli et al. [] proposed a method called timedelay-aracne. it tries to extract dependencies between two genes at different time delays, providing a measure of these dependencies in terms of mutual information. timedelay-aracne can infer […]

PMCID: 4816347
PMID: 27031641
DOI: 10.1371/journal.pone.0152648

[…] (him) metric to quantify network differences, the effectiveness of the dtw-mic approach is demonstrated on a set of four synthetic and one transcriptomic datasets, also in comparison to timedelay aracne and transfer entropy., genenetweaver yeast & e. coli data the datasets (network and time-course) for the four gene net weaver examples can be accessed on figshare with doi […]

PMCID: 4673427
PMID: 26696898
DOI: 10.3389/fphys.2015.00364

[…] longitudinal transcriptomics derived from cells/tissues of an individual including healthy and diseased states are the ideal resources to assemble an individualized grn. zoppoli et al. () introduced timedelay-aracne to infer grns specifically from time-course data. such aracne-inferred grn provides a personalized map, with which one can locate the genetic mutations identified […]

PMCID: 4290726
PMID: 25521243
DOI: 10.1186/1752-0509-8-S4-S6

[…] grn. in 2010, a dynamic version of aracne (algorithm for the reconstruction of accurate cellular networks) was introduced to infer time-delayed dependencies among genes []. their method, called timedelay aracne (or td-aracne), is able to reconstruct time-delayed dependencies effectively. in 2012, morshed et al. proposed a framework to infer instantaneous and time-delayed genetic […]


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TimeDelay-ARACNE institution(s)
Department of Biological and Environmental Studies, University of Sannio, Benevento, Italy; Biogem scarl, Institute for Genetic Research "Gaetano Salvatore", Ariano Irpino (Avellino), Italy
TimeDelay-ARACNE funding source(s)
This work was supported by Italian Ministry MIUR (PRIN 20085CH22F).

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