Igraph protocols

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Igraph specifications

Information


Unique identifier OMICS_16451
Name Igraph
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++, Python, R
Computer skills Advanced
Version 1.0.0
Stability Stable
Maintained Yes

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  • person_outline Gabor Csardi <>

Igraph in pipelines

 (20)
2018
PMCID: 5799258
PMID: 29402898
DOI: 10.1038/s41598-018-20515-w

[…] lower than 0.1%) were removed before the network analysis as previously described. briefly, microbial species-level co-occurrence networks were conducted in the r environment using the vegan, igraph, and hmisc packages. positive co-occurrence events were considered if the otus demonstrated the spearman’s correlation coefficient higher than 0.6 and statistically significant (p < 0.01),. […]

2018
PMCID: 5821391
PMID: 29420542
DOI: 10.1371/journal.pntd.0006248

[…] may lead the network to break down without further links of the parasites to the remaining hosts. we built and obtained indexes of the network structure on the r programming environment [] using the igraph [], bipartite [], and picante [] packages. 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 […]

2017
PMCID: 5363043
PMID: 28330499
DOI: 10.1186/s13073-017-0417-1

[…] []. for the single tissue analysis (e.g., lung network), we considered only the largest connected component of each network and performed spin-glass community detection as implemented in 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 […]

2017
PMCID: 5513928
PMID: 28769962
DOI: 10.3389/fpls.2017.01259

[…] for pairwise genes from ppi database was extracted. the ppi matrix with evidence number were presented as heatmap using r package “pheatmap,” and the graph network were displayed using r package “igraph.”, sl and mp participated in the design of the study. sl and xy analyzed the rna-seq data. zc, xly, mbr, and wl carried out the molecular biology experiments. all authors read and approved […]

2017
PMCID: 5557790
PMID: 28855896
DOI: 10.3389/fmicb.2017.01563

[…] the relationships among microbial taxa, samples, and variables and to test the significance of correlations between variables and microbial distribution. network analysis was performed using the igraph package to present the age effect on microbial interactions (), and spls regression was performed to show otus related to response variables using the spls package (). phylogenetic trees […]

Igraph in publications

 (791)
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] baits. the network was partitioned into distinct protein communities by maximizing the modularity score of the network over all possible partitions using the “cluster_optimal” function of the “igraph” package in r. gene ontology (go) term enrichment analysis for each separate network community was performed. enrichment was computed with the topgo package from r, using the default algorithm […]

PMCID: 5942835
PMID: 29742156
DOI: 10.1371/journal.pone.0197144

[…] von neumann neighborhood (i.e., each cell has four neighbors in the north, south, east, and west). to find the connected components, we used the “decompose.graph” function provided by the r package ‘igraph’ []. this function takes a list of the pairs of connected cells and returns the list of the connected components. we refer to each connected component as cluster. we obtained 24165 and 24707 […]

PMCID: 5943561
PMID: 29774217
DOI: 10.3389/fvets.2018.00071

[…] aim of correlating idealized networks with disease transmission times, we generated maximally complete, unweighted, undirected networks for groups of size 3–200 in r, version 3.3.2 () with packages igraph (), statnet (), and functions that we developed and distribute in enss. we then simulated si models (with a per contact transmission rate, β, of 0.10, and per capita interactions per day set […]

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

[…] 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 and thus were named […]

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

[…] first, we built unweighted bipartite networks to analyze the threats associated with species’ extinctions 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 […]

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