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Citations per year

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

This map represents all the scientific publications referring to GraphCrunch per scientific context
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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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Maintainer


  • person_outline Natasa Przulj

Publications for GraphCrunch

GraphCrunch citations

 (18)
library_books

Modular Organization of Residue Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

2017
Genome Biol Evol
PMCID: 5388290
PMID: 28338825
DOI: 10.1093/gbe/evx036

[…] m 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 and RGF-distance-based […]

library_books

Combinatorial algorithm for counting small induced graphs and orbits

2017
PLoS One
PMCID: 5300269
PMID: 28182743
DOI: 10.1371/journal.pone.0171428

[…] om 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 of countin […]

library_books

An Examination of Not For Profit Stakeholder Networks for Relationship Management: A Small Scale Analysis on Social Media

2016
PLoS One
PMCID: 5053609
PMID: 27711236
DOI: 10.1371/journal.pone.0163914

[…] As discussed, the output from the pairwise network comparison implemented with GraphCrunch 2 allows us to report, among other measures, GDD agreement (arithmetic mean), and RGF distance, to assess local-level topological similarity—along with Pearson and Spearman correlations of […]

library_books

Wnt signal transduction pathways: modules, development and evolution

2016
BMC Syst Biol
PMCID: 4977476
PMID: 27490822
DOI: 10.1186/s12918-016-0299-7

[…] as been the topological similarity between the two species-specific pathways. SP(x,y) has been calculated by the GRAph ALigner algorithm (GRAAL) developed by Kuchaiev et al. [] and implemented in the GraphCrunch2 software []. SP(x,y) is nothing but Edge Correctness (EC) value between a pair of species-specific Wnt STPs. Edge correctness is the percentage of edges in the first graph that are aligne […]

library_books

Distinctive Behaviors of Druggable Proteins in Cellular Networks

2015
PLoS Comput Biol
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 into ‘isomorphis […]

library_books

Exploring the structure and function of temporal networks with dynamic graphlets

2015
Bioinformatics
PMCID: 4765862
PMID: 26072480
DOI: 10.1093/bioinformatics/btv227

[…] mporal 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, as permitte […]


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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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