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CopTea specifications

Information


Unique identifier OMICS_21884
Name CopTea
Alternative name Combinatorial OPTimization based Enrichment Analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.4.0
Stability Stable
Maintained Yes

Subtools


  • CEA (Combination-based Enrichment Analysis)
  • NetGen

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Versioning


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Maintainers


  • person_outline Ling-Yun Wu
  • person_outline Ling-Yun Wu
  • person_outline Duanchen Sun

Publications for Combinatorial OPTimization based Enrichment Analysis

CopTea citations

 (8)
library_books

Mechanical Characterization of the Vessel Wall by Data Assimilation of Intravascular Ultrasound Studies

2018
Front Physiol
PMCID: 5882902
PMID: 29643815
DOI: 10.3389/fphys.2018.00292

[…] pressure equation. For the analysis of the proposed approach, four patient-specific 3D geometries were obtained using the technique described in section 2.1.4. These geometries were discretized using Netgen 3D using a characteristic element size ranging from 10μm to 40μm, resulting in meshes with 6,521, 7,516, 4,835, and 3,808 nodes for the cases 1–4, respectively. All these steps are performed us […]

library_books

Understanding biological systems through the lens of data

2017
BMC Syst Biol
PMCID: 5615238
PMID: 28950868
DOI: 10.1186/s12918-017-0450-0

[…] on in the Drosophila large intestine in order to better interpret related experimental findings of this biological phenomenon.Sun et al. proposed a novel network-based probabilistic generative model, NetGen, to perform the functional enrichment analysis. An additional protein-protein interaction (PPI) network was explicitly used to assist the identification of significantly enriched GO terms. NetG […]

library_books

Patients experiencing statin induced myalgia exhibit a unique program of skeletal muscle gene expression following statin re challenge

2017
PLoS One
PMCID: 5542661
PMID: 28771594
DOI: 10.1371/journal.pone.0181308

[…] d to the likelihood of finding the focus genes among a similar number of genes randomly selected from the global gene network (https://www.ingenuity.com/wp-content/themes/ingenuity-qiagen/pdf/ipa/IPA-netgen-algorithm-whitepaper.pdf). A useful feature of IPA is the identification of major canonical pathways with greater than expected enrichment with the genes of interest. IPA analysis identified fi […]

library_books

Simulating and Summarizing Sources of Gene Tree Incongruence

2016
Genome Biol Evol
PMCID: 4898792
PMID: 27017528
DOI: 10.1093/gbe/evw065

[…] trees under a range of hybridization scenarios which can then be compared with patterns of gene tree incongruence in real datasets.There are some current simulators of hybrid evolution, in particular Netgen () specifically models hybrid speciation. Netgen is a forward-in-time simulator, but it only provides limited control over how genetic distance between pairs of species affects their chance of […]

library_books

Characterization of phylogenetic networks with NetTest

2010
BMC Bioinformatics
PMCID: 2880032
PMID: 20487540
DOI: 10.1186/1471-2105-11-268

[…] algorithm" that can be exported in NEXUS format (*.nex) and feeded directly to NetTest.• Extended Newick (eNewick) []: This is the type of representation used for the directed networks simulated with Netgen [] or estimated with Phylonet []. The leftmost occurrence of each hybrid node in an eNewick string corresponds to the full description of the subnetwork rooted at that node.• DIMACS standard [] […]

library_books

Extended Newick: it is time for a standard representation of phylogenetic networks

2008
BMC Bioinformatics
PMCID: 2621367
PMID: 19077301
DOI: 10.1186/1471-2105-9-532

[…] omputational biologist might also benefit as well, given the importance of standards for tool development [].A first proposal of a compact representation for phylogenetic networks can be found in the NetGen package for phylogenetic networks [], where a phylogenetic network with k hybrid nodes is represented as a single phylogenetic tree in Newick format but with k repeated nodes. For example, the […]

Citations

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CopTea institution(s)
IAM, MADIS, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, China
CopTea funding source(s)
Supported by the Strategic Priority Research Program of the Chinese Academy of Sciences [No. XDB13040600] and the National Natural Science Foundation of China [Nos 11631014, 91730301, 11661141019].

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