Gephi statistics

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Citations per year

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Popular tool citations

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Associated diseases


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Gephi specifications


Unique identifier OMICS_16845
Name Gephi
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Medium
Version 0.9.1
Stability Stable
Maintained Yes



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  • person_outline Mathieu Bastian <>

Gephi in pipelines

PMCID: 5799258
PMID: 29402898
DOI: 10.1038/s41598-018-20515-w

[…] the spearman’s correlation coefficient higher than 0.6 and statistically significant (p < 0.01),. the constructed networks were further optimized by the interactive visualization platform gephi. the r software was also employed for the heat map plotting to visualize profiles of the co-occurring microbial species in each sample. mega 6.06 was used to construct the phylogenetic tree […]

PMCID: 5821391
PMID: 29420542
DOI: 10.1371/journal.pntd.0006248

[…] the resilience of the networks of each genus and stage of ticks after recursive removal of host nodes was evaluated with the package netswan for r []. visualization of the networks was done in gephi v0.91 []., to analyze the relationships between ticks and hosts with evidence of a potential role in cchfv circulation, we compiled a list of tick species distributed over the geographical […]

PMCID: 5270224
PMID: 28126036
DOI: 10.1186/s13059-017-1156-8

[…] of resulting gene clusters were performed using cluego [], setting the kappa score to 0.4 and the cutoff for statistical significance at bh-corrected p < 0.05. all networks were visualized using gephi []., associations between both gene expression and dna methylation levels with donor-specific quantitative traits, cellular parameters, as well as weather and seasonal effects were assessed […]

PMCID: 5363043
PMID: 28330499
DOI: 10.1186/s13073-017-0417-1

[…] the igraph r package [] to obtain the functional modules. we annotated functional modules using g:profiler [] using all genes in a module as a query. all networks in this work were visualized using gephi []. the network layout was determined by community membership, the strength of connections between communities, and finally the interactions between individual genes. the lung network node […]

PMCID: 5479047
PMID: 28637485
DOI: 10.1186/s40168-017-0277-3

[…] microbial abundance datasets [], was used to cluster the log10-transformed abundances. the otu network files generated by qiime were input into cytoscape ( and gephi ( modularity analysis, betweenness centrality, and degree indices were used to format and color the layout of the network., additional file 1: table s1. additional file 2: […]

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Gephi in publications

PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] in at least one complex were used as the background population. p-values were corrected for multiple testing as explained above. protein interaction networks were visualized using cytoscape and gephi. detailed information about all 960 identified interactors of mll-fusion proteins is provided in supplementary data ., molm-13 cells transduced with mini-pools of retroviral vectors […]

PMCID: 5931971
PMID: 29720620
DOI: 10.1038/s41467-018-04104-z

[…] in. networks of relatedness were generated using networkx (, a python package for the creation, manipulation, and study of complex networks, and visualized using gephi, an open-source software for network visualization and analysis., calculations of ec50, student’s t-test, one-way analysis of variance and correlations were performed using graphpad prism […]

PMCID: 5923273
PMID: 29703908
DOI: 10.1038/s41598-018-25042-2

[…] interaction information of 8,177 proteins. essentially, the interaction information of all the proteins, weighted by the combined scores from different parameters as per string, was imported into gephi version 0.9.1 for visualization. the interactome of cancer proteins, thus constructed, can be perceived as the protein interaction network (pin) represented by an undirected graph g = (v, e) […]

PMCID: 5922530
PMID: 29702660
DOI: 10.1371/journal.pone.0196211

[…] measures the extent to which an individual dominates the network (high centralization), or if relationships are more evenly dispersed through the network (low). network data were visualized using gephi [] and analyzed using igraph [], a package for r., response rate and network member classification information is shown in . there were 25 identified sc members from sus. of these, 15 consented […]

PMCID: 5913315
PMID: 29686360
DOI: 10.1038/s41598-018-24733-0

[…] and risks of extinction. networks were created with r software (version 3.3.1) using igraph and rgexf packages,. then, network structures were explored and visualized with the interactive platform gephi using a forceatlas 2 layout. a layout is an algorithm that positions nodes in a 2-d or 3-d space. forceatlas 2 layout allows the network to be visualized based on the forces of attraction […]

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Gephi reviews

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