GraphCrunch protocols

View GraphCrunch computational protocol

GraphCrunch statistics

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GraphCrunch specifications

Information


Unique identifier OMICS_15579
Name GraphCrunch
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Medium
Version 2.1.1
Stability Stable
Requirements
Perl, Xdialog
Source code URL http://www0.cs.ucl.ac.uk/staff/natasa/graphcrunch2/GraphCrunch2.1.1Code.zip
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/GraphCrunch

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  • person_outline Natasa Przulj <>

Publications for GraphCrunch

GraphCrunch in pipelines

 (2)
2015
PMCID: 4317708
PMID: 25651890
DOI: 10.1038/srep08275

[…] with p-value of 0.05, and the computed values of spearman correlation coefficients with r-statistics package (www.r-project.org) were feed into cytoscape network analysis software and gephi. the graphcrunch2 software was applied to further compare the reconstructed milk microbiome network with several standard models of complex networks. the results of network analysis are exhibited […]

2012
PMCID: 3471511
PMID: 23087704
DOI: 10.3389/fgene.2012.00208

[…] resulted networks were analyzed by comparison to each other, and by comparison to randomly generated network null models of same graph constraints. this was achieved via a network analysis utility graphcrunch2 (milenkovic et al., ). the k-clique community finding tool “cfinder” was used to grab the community structures (closely interlinked sub-graphs) in the core molecular network (k = 3). […]


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GraphCrunch in publications

 (15)
PMCID: 5388290
PMID: 28338825
DOI: 10.1093/gbe/evx036

[…] networks—where graphlets are small substructures of large networks ()—relative graphlet frequency distance (rgf-distance) and graphlet degree distribution agreement (gdd-agreement), estimated using graphcrunch software package (). a high gdd-agreement and low rgf-distance denote a strong structural similarity between the original network and the random model., gdd-agreement […]

PMCID: 5300269
PMID: 28182743
DOI: 10.1371/journal.pone.0171428

[…] erdős-rényi graphs., we measured the time needed for counting node- and edge-orbits with the orca algorithm and compared it to a bruteforce enumeration. for the latter we used an implementation from graphcrunch. orca outperforms exhaustive enumeration by an order of magnitude (tables and ). the running times for counting node-orbits and edge-orbits are practically the same in the case […]

PMCID: 4689399
PMID: 26699810
DOI: 10.1371/journal.pcbi.1004597

[…] protein’s neighbors are in the same community and therefore the protein favors intra-community communication while a low vm number indicates the protein favors inter-community communication. we used graphcrunch [] to calculate subgraphs previously described as a means of fragmenting networks into smaller graphlets [] (fig b in ). the nodes within these graphlets can be classified […]

PMCID: 4765862
PMID: 26072480
DOI: 10.1093/bioinformatics/btv227

[…] network as well as for each individual node. to obtain static or static-temporal graphlet counts of the entire aggregated network or of individual temporal snapshots, respectively, one can use graphcrunch (; )., as different input parameter values may be optimal for different network types (e.g. networks from different domains), we recommend testing several different combinations, […]

PMCID: 4317708
PMID: 25651890
DOI: 10.1038/srep08275

[…] computed with network analysis software packages (e.g., cytoscape, gephi) offer informative insights on the patterns in biological data. complex network alignment algorithms and software (e.g., graphcrunch2) can further be utilized to compare biological networks under different treatments., the 16s rrna sequence data sets of human milk were collected by hunt et al (2011). specifically, […]


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GraphCrunch institution(s)
Department of Computing, Imperial College, London, UK; Department of Computer Science, University of California, Irvine, CA, USA
GraphCrunch funding source(s)
This project was supported by NSF CAREER IIS- 0644424 and NSF CDI OIA-1028394 grants.

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