
igraph
 Referenced in 215 articles
[sw07066]
 igraph is a software package for complex network analysis and graph theory, with an emphasis...

NetworkX
 Referenced in 168 articles
[sw00616]
 structure, dynamics, and functions of complex networks...

Graphs
 Referenced in 109 articles
[sw12277]
 compact routing and distance labeling schemes in networking and distributed computing and for metric embeddings ... significance such as planar graphs and complex networks...

Brain Connectivity Toolbox
 Referenced in 90 articles
[sw26516]
 brainconnectivitytoolbox.net) is a MATLAB toolbox for complexnetwork (graph) analysis of structural and functional brain...

node2vec
 Referenced in 83 articles
[sw27202]
 link prediction in several realworld networks from diverse domains. Taken together, our work represents ... taskindependent representations in complex networks...

Neural Network Toolbox
 Referenced in 178 articles
[sw07378]
 Network Toolbox. Neural Network Toolbox™ provides functions and apps for modeling complex nonlinear systems that...

MCODE
 Referenced in 49 articles
[sw35748]
 method for finding molecular complexes in large protein interaction networks. Results: This paper describes ... large proteinprotein interaction networks that may represent molecular complexes. The method is based ... interest without considering the rest of the network and allows examination of cluster interconnectivity ... which is relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces...

Gephi
 Referenced in 64 articles
[sw12110]
 exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. Runs...

ARACNE
 Referenced in 38 articles
[sw17200]
 gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing ... genomewide ”reverse engineering” of such networks have been successful only for lower eukaryotes with ... scale up to the complexity of regulatory networks in mammalian cells, yet general enough ... complex topologies. We assess ARACNE’s ability to reconstruct transcriptional regulatory networks using both...

REVEAL
 Referenced in 29 articles
[sw36999]
 reverse engineering algorithm for inference of genetic network architectures. Given the immanent gene expression mapping ... principle, to completely infer a complex regulatory network architecture from input/output patterns of its variables ... this study is limited to synchronous Boolean networks, the algorithm is generalizable to include multi ... problem may enable indepth analysis of complex dynamic systems in biology and other fields...

Kavosh
 Referenced in 12 articles
[sw29733]
 algorithm for finding network motifs. Background: Complex networks are studied across many fields of science ... significantly in higher frequencies than in random networks. They have recently gathered much attention ... uncover structural design principles of complex networks. Existing algorithms for finding network motifs are extremely...

QuACN
 Referenced in 8 articles
[sw07971]
 package QuACN: QuACN: Quantitative Analysis of Complex Networks. Quantitative Analysis of Complex Networks. This package ... topological network measures to analyze complex Networks structurally...

pyunicorn
 Referenced in 8 articles
[sw19314]
 Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package ... introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package ... data analysis and modeling from complex network theory and nonlinear time series analysis. exttt{pyunicorn ... this structure using advanced methods of complex network theory such as measures and models...

NetworKit
 Referenced in 13 articles
[sw35938]
 tool suite for largescale complex network analysis. NetworKit is a growing opensource toolkit...

FANMOD
 Referenced in 19 articles
[sw26134]
 than would be expected for a random network. They have recently gathered much attention ... uncover structural design principles of complex biological networks. FANMOD is a tool for fast network...

PDENet
 Referenced in 91 articles
[sw36963]
 propose a new feedforward deep network, called PDENet, to fulfill two objectives ... same time: to accurately predict dynamics of complex systems and to uncover the underlying hidden ... learning convolution kernels (filters), and apply neural networks or other machine learning methods to approximate...

DOULION
 Referenced in 12 articles
[sw30192]
 significant role in complex network analysis. Metrics frequently computed such as the clustering coefficient...

jHoles
 Referenced in 7 articles
[sw15020]
 jHoles: A tool for understanding biological complex networks via clique weight rank persistent homology. Complex ... networks equipped with topological data analysis are one of the promising tools in the study ... studying the connectivity features of complex networks. jHoles fills the lack of an efficient implementation...

Cytoscape
 Referenced in 81 articles
[sw09080]
 other molecular states; and to link the network to databases of functional annotations. The Core ... complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network...

LeZiupdate
 Referenced in 18 articles
[sw01541]
 personal mobility tracking in PCS networks The complexity of the mobility tracking problem...