• igraph

  • Referenced in 163 articles [sw07066]
  • igraph is a software package for complex network analysis and graph theory, with an emphasis...
  • NetworkX

  • Referenced in 116 articles [sw00616]
  • structure, dynamics, and functions of complex networks...
  • Graphs

  • Referenced in 104 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 71 articles [sw26516]
  • brain-connectivity-toolbox.net) is a MATLAB toolbox for complex-network (graph) analysis of structural and functional brain...
  • Neural Network Toolbox

  • Referenced in 175 articles [sw07378]
  • Network Toolbox. Neural Network Toolbox™ provides functions and apps for modeling complex nonlinear systems that...
  • MCODE

  • Referenced in 47 articles [sw35748]
  • method for finding molecular complexes in large protein interaction networks. Results: This paper describes ... large protein-protein 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...
  • node2vec

  • Referenced in 33 articles [sw27202]
  • link prediction in several real-world networks from diverse domains. Taken together, our work represents ... task-independent representations in complex networks...
  • Gephi

  • Referenced in 48 articles [sw12110]
  • exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. Runs...
  • ARACNE

  • Referenced in 35 articles [sw17200]
  • gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing ... genome-wide ”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 28 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 in-depth analysis of complex dynamic systems in biology and other fields...
  • 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...
  • Kavosh

  • Referenced in 8 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...
  • LeZi-update

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

  • Referenced in 6 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 73 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...
  • DOULION

  • Referenced in 10 articles [sw30192]
  • significant role in complex network analysis. Metrics frequently computed such as the clustering coefficient...
  • NetworKit

  • Referenced in 10 articles [sw35938]
  • tool suite for large-scale complex network analysis. NetworKit is a growing open-source toolkit...
  • FANMOD

  • Referenced in 14 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...
  • CONTEST

  • Referenced in 19 articles [sw12738]
  • toolbox for MATLAB. Large, sparse networks that describe complex interactions are a common feature across ... that capture key properties of real-life networks. These models provide realistic, parametrized matrices...
  • pyunicorn

  • Referenced in 5 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...