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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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Maintainer


  • person_outline Gabor Csardi

Igraph citations

 (298)
library_books

MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

2018
Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] fusion 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 […]

library_books

Effective Network Size Predicted From Simulations of Pathogen Outbreaks Through Social Networks Provides a Novel Measure of Structure Standardized Group Size

2018
PMCID: 5943561
PMID: 29774217
DOI: 10.3389/fvets.2018.00071

[…] t 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 at […]

library_books

Insular threat associations within taxa worldwide

2018
Sci Rep
PMCID: 5913315
PMID: 29686360
DOI: 10.1038/s41598-018-24733-0

[…] ar regions was connected to threats with an associated weight depending on the number of insular species threatened by each threat in that region. As above, networks were created using the R packages igraph and rgexf, and network structures were explored and visualized with Gephi software using a Geo Layout, which uses latitude and longitude coordinates to set the node position in the graphic spac […]

call_split

Quantifying ecological impacts of mass extinctions with network analysis of fossil communities

2018
Proc Natl Acad Sci U S A
PMCID: 5960297
PMID: 29686079
DOI: 10.1073/pnas.1719976115
call_split See protocol

[…] taxa (i.e., taxa of uncertain rank and those with subordinate names), and taxa lacking connections or occurring in small isolated clusters.The datasets were analyzed in RStudio using functions in the igraph, GGally, network, ggplot2, and sunburstR packages. Network graphs were generated using the ggnet2 function of ggplot2 and its default parameters, and nodes of equal size were placed without sel […]

library_books

Recurrent acquisition of cytosine methyltransferases into eukaryotic retrotransposons

2018
Nat Commun
PMCID: 5890265
PMID: 29632298
DOI: 10.1038/s41467-018-03724-9

[…] active lineages there were among the young transposons, we built a network using the identity values as edges and the sequences as nodes, obtaining the total number of orthologous clusters using the 'igraph' package for R in CRAN.To characterise the evolution of specific transposon subfamilies, we first clustered transposable element sequences belonging to all Symbiodinium species using blastp pai […]

library_books

Mapping human pluripotent stem cell differentiation pathways using high throughput single cell RNA sequencing

2018
Genome Biol
PMCID: 5887227
PMID: 29622030
DOI: 10.1186/s13059-018-1426-0

[…] ns from Seurat were analyzed by Monocle v2.3.6 (pseudotime analysis) []. TFs from AnimalTFDB [] and surface genes [] were used to filter the gene lists. The cell–cell interactions were constructed by igraph v1.12 as previously reported []. The count of cell–cell interactions was based on the ligands-receptors pairings []. We used DAVID [] to perform GO and KEGG analysis. GO terms were visualized b […]

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