CoNet statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CoNet
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Tool usage distribution map

This map represents all the scientific publications referring to CoNet per scientific context
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Associated diseases

This word cloud represents CoNet usage per disease context
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Protocols

CoNet specifications

Information


Unique identifier OMICS_16020
Name CoNet
Alternative name Co-occurrence Network
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 3.0
Stability Beta
Requirements
Cytoscape
Maintained Yes

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Documentation


Maintainer


  • person_outline Karoline Faust

Information


Unique identifier OMICS_16020
Name CoNet
Alternative name Co-occurrence Network
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Programming languages Java
Computer skills Basic
Stability Stable

Versioning


No version available

Documentation


Maintainer


This tool is not maintained anymore.

Publication for Co-occurrence Network

CoNet citations

 (44)
library_books

Coral Bacterial Core Abundance and Network Complexity as Proxies for Anthropogenic Pollution

2018
Front Microbiol
PMCID: 5934943
PMID: 29755445
DOI: 10.3389/fmicb.2018.00833

[…] om M. hispida. Significant correlations between OTUs with a minimum occurrence of 8 were determined using Pearson’s correlation and Spearman’s correlation (between -0.50 and 0.50, p < 0.05) using the CoNet app () in Cytoscape v.3.0.2 ().A Venn diagram from site-stable bacterial populations (persistent OTUs found at each reef/sampling point) was obtained using the web-based tool InteractiVenn (). […]

library_books

Microbiome and Culture Based Analysis of Chronic Rhinosinusitis Compared to Healthy Sinus Mucosa

2018
Front Microbiol
PMCID: 5932350
PMID: 29755418
DOI: 10.3389/fmicb.2018.00643

[…] rise relevant human pathogens. Members of the genus Porphyromonas can cause periodontitis and root canal abscesses (Nickles et al., ; Nobrega et al., ; Tomas et al., ) and were associated with CRS in CoNet analyses in a recent meta-analysis of the 16S rRNA sequencing data (Wagner Mackenzie et al., ). Members of the genera Stenotrophomonas and Pseudomonas are frequently involved in hospital acquire […]

library_books

Structure and co occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

2018
Sci Rep
PMCID: 5897386
PMID: 29651160
DOI: 10.1038/s41598-018-23931-0

[…] cological interactions was obtained from patterns of occurrence of distinctive 16 S rRNA sequences, physicochemical parameters and soil nutrient content. Co-occurrence networks were constructed using CoNet algorithm, as described previously, (Supplementary information Fig. ).The network of OTUs from Section 1 (Supplementary Dataset Table ) contained 484 nodes (476 OTUs and 8 variables) connected b […]

library_books

Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits

2018
Front Microbiol
PMCID: 5902543
PMID: 29692775
DOI: 10.3389/fmicb.2018.00733

[…] nce, partitioning around medoid clustering (PAM), and Calinski-Harabasz Index (CH) at the genus level (), and visualized via principal coordinate analysis (PCoA).Network speculation was performed via CoNet (). Co-occurrence networks were constituted based on the union of subnets (stomach-jejunum, jejunum-ileum, ileum-cecum, and cecum-colon) to display the relationships of gut microbiota within sit […]

call_split

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs

2018
Sci Rep
PMCID: 5871783
PMID: 29593306
DOI: 10.1038/s41598-018-23373-8
call_split See protocol

[…] ble. Multiple hypotheses were adjusted by Benjamini and Hockberg false discovery rate (FDR) and significant associations were considered below a q-value threshold of 0.1.Correlation network analysis (CoNet) was used to evaluate the impact of yeast supplementation on the co-occurrence pattern of cecum and colon microbial communities (comparison made between control-control and yeast-yeast groups). […]

call_split

Close Link Between Harmful Cyanobacterial Dominance and Associated Bacterioplankton in a Tropical Eutrophic Reservoir

2018
Front Microbiol
PMCID: 5857610
PMID: 29593677
DOI: 10.3389/fmicb.2018.00424
call_split See protocol

[…] ed relevant correlations those with p < 0.001 and r > 0.6. The visualization of these correlations was made with the Cytoscape package version 3.4.0 (available at: www.cytoscape.org) using the plugin CoNet. The r-value (>0.6) was selected to support the generation of an edge-weighted spring-embedded network (Assenov et al., ). The network included the classified OTUs which contributed with at leas […]


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CoNet funding source(s)
This work was supported in part by NIH CA139193, NIH U54HG004969, the Crohn’s and Colitis Foundation of America, and the Juvenile Diabetes Research Foundation, NSF DBI-1053486, ARO W911NF-11-1-0473, NIH 1R01HG005969 and the Research Foundation - Flanders.

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