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Centrality exploration software tools │ Biochemical network

Here, we surveyed bioinformatics software tools for network centrality inference. The elucidation of whole-cell regulatory, metabolic, interaction and other biological networks generates the need for a meaningful ranking of network elements.…
NetworkAnalyzer
Desktop

NetworkAnalyzer

Allows comprehensive network topology analysis. NetworkAnalyzer is a plugin of…

Allows comprehensive network topology analysis. NetworkAnalyzer is a plugin of Cytoscape. The software performs a comprehensive analysis of network topologies without requiring advanced knowledge in…

CoTB
Algorithm

CoTB

Combines Den1, Den2, BC, IDC, LC, DOS and subcellular localization score (SLS).…

Combines Den1, Den2, BC, IDC, LC, DOS and subcellular localization score (SLS). CoTB uses a random forest model to obtain a probability score for the proteins being essential. The performances of the…

SANTA
Desktop

SANTA Spatial Analysis of Network Associations

A package which provides methods for measuring the strength of association…

A package which provides methods for measuring the strength of association between a network and a phenotype. SANTA quantifies the strength of association between a gene set and a network, and…

CytoNCA
Desktop

CytoNCA

A convenient app for network centrality analysis. CytoNCA supports eight…

A convenient app for network centrality analysis. CytoNCA supports eight typical centralities: Betweeness Centrality [1], Closeness Centrality [2], Degree Centrality [3], Eigenvector Centrality [4],…

CINNA
Desktop

CINNA Central Informative Nodes in Network Analysis

Calculates, compares, assorts, and visualizes network centrality measures…

Calculates, compares, assorts, and visualizes network centrality measures together. CINNA is an R package that provides a collection of functions. This package provides different visualization…

RINspector
Desktop

RINspector

Combines residue interaction network (RIN) centrality analyses with direct…

Combines residue interaction network (RIN) centrality analyses with direct visualization of the predicted local flexibility of the associated sequence. RINspector is a Cytoscape app that links the…

ATria
Desktop

ATria Ablatio Triadum

Finds leaders, villains and bridges within a signed, weighted social network.…

Finds leaders, villains and bridges within a signed, weighted social network. ATria is an iterative extension of a payoff model using social networking principles and in the process overcome…

CentiLib
Desktop

CentiLib

A Java-library and user-friendly plug-in for the computation and investigation…

A Java-library and user-friendly plug-in for the computation and investigation of weighted and unweighted centralities in biological networks. CentiLib provides 17 different node centrality and four…

CentiScaPe
Desktop

CentiScaPe Centralities for Cytoscape

A Cytoscape plug-in for calculating network centralities with numerical and…

A Cytoscape plug-in for calculating network centralities with numerical and graphical output. CentiScaPe computes several network centrality parameters and allows the user to analyze existing…

RINalyzer
Desktop

RINalyzer

Provides versatile and interactive structure analysis tools for residue…

Provides versatile and interactive structure analysis tools for residue interaction networks (RINs) and enables dynamic 2D and 3D views. RINalyzer is a software tool for the automatized generation,…

MCDS
Desktop

MCDS Minimum Connected Dominating Set

Allows to study pluripotency network for mouse embryonic stem cells and gene…

Allows to study pluripotency network for mouse embryonic stem cells and gene regulatory networks of the model organisms E. coli and S. cerevisiae. MCDS is useful in the case of networks related to…

cyto-Hubba
Desktop
Web

cyto-Hubba

A Java plugin for Cytoscape, a facilitated platform for the analysis and…

A Java plugin for Cytoscape, a facilitated platform for the analysis and visualization of molecular interaction networks based on web application, Hubba. cytoHubba provides a user-friendly interface…

CentiServer
Web
Desktop

CentiServer

A comprehensive online resource that provides over 110 definitions of different…

A comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. Centiserve is also an R…

CentiBiN
Desktop
Web

CentiBiN Centralities in Biological Networks

A tool for the computation and exploration of centralities in biological…

A tool for the computation and exploration of centralities in biological networks such as protein-protein interaction networks. CentiBiN computes 17 different centralities for directed or undirected…

Statnet
Web
Desktop

Statnet

Allows users to analyze statistical network. Statnet is a software which is…

Allows users to analyze statistical network. Statnet is a software which is available both as a R package and as a web application. It supplies a framework for exponential-family random graph models…

AllegroGraph
Desktop

AllegroGraph

Allows to build Semantic Web applications. AllegroGraph is a database and an…

Allows to build Semantic Web applications. AllegroGraph is a database and an application framework which enables the extraction of sophisticated decision insights and predictive analytics from their…

UCINET
Desktop

UCINET

Uses for the analysis of social network data. UCINET is menu-driven Windows…

Uses for the analysis of social network data. UCINET is menu-driven Windows program that implements a diverse collection of network analysis techniques, in addition to traditional statistical…

tnet
Desktop

tnet

Analyse weighted networks, two-mode networks, and longitudinal networks…

Analyse weighted networks, two-mode networks, and longitudinal networks (datasets with time-stamped ties). Tnet is an R package that uses three forms of data structures: simple weighted data,…

sna
Desktop

sna

Implements recent advances in the statistical modelling of networks. Sna…

Implements recent advances in the statistical modelling of networks. Sna provides a comprehensive framework for ergm-based network modelling, including tools for model estimation, model evaluation,…

RBGL
Desktop

RBGL

Uses as a fairly extensive and comprehensive interface to the graph algorithms…

Uses as a fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. RBGL is an R package that consists of a number of interfaces to the Boost C++ library…

qgraph
Desktop

qgraph

Provides an interface to visualize data through network modelling techniques.…

Provides an interface to visualize data through network modelling techniques. Qgraph is an R package that accommodates capacities for spotting patterns by visualizing data in a novel way: through…

MultiNet
Desktop

MultiNet

Offers context-sensitive, interactive, on-line help, and always presents a…

Offers context-sensitive, interactive, on-line help, and always presents a color graphic representation of the data or the results of analysis. MultiNet is an interactive menu-driven program for…

FUGA
Desktop

FUGA Functional Genomics Assistant

A MATLAB toolbox for inference and analysis of biological and cellular…

A MATLAB toolbox for inference and analysis of biological and cellular networks, biological relationships, graph topology analysis, random network simulation, network clustering, and functional…

Interference
Desktop

Interference

A Cytoscape plug-in for virtual knock-out experiments on complex networks.…

A Cytoscape plug-in for virtual knock-out experiments on complex networks. Interference is a Centralities based measure. Interference plug-in computes the Interference values for the following…

SBEToolbox
Desktop

SBEToolbox Systems Biology and Evolution Toolbox

An open-source Matlab toolbox for biological network analysis. SBEToolbox takes…

An open-source Matlab toolbox for biological network analysis. SBEToolbox takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and…

ModuLand
Desktop

ModuLand

A tool for determination of hierarchical layers of overlapping network modules…

A tool for determination of hierarchical layers of overlapping network modules and community centrality. The ModuLand Cytoscape plug-in provides a user-friendly and efficient method to identify and…

BCT
Desktop

BCT Brain Connectivity Toolbox

A Matlab toolbox for analysis of complex brain networks. The toolbox contains…

A Matlab toolbox for analysis of complex brain networks. The toolbox contains network analysis functions and complex brain network datasets. These measures are increasingly used to characterize…

WebGraph
Desktop

WebGraph

Provides simple ways to manage very large graphs, exploiting modern compression…

Provides simple ways to manage very large graphs, exploiting modern compression techniques. WebGraph is a framework for graph compression aimed at studying web graphs. It is currently made of A set…

Visone
Desktop

Visone VIsual SOcial NEtworks

Uses as a software for the visual creation, transformation, exploration,…

Uses as a software for the visual creation, transformation, exploration, analysis, and representation of network data. Visone is a long-term research project, in which models and algorithms to…

SocNetV
Desktop

SocNetV Social Network Visualizer

Offers resources to draw social networks with a few clicks on a virtual canvas,…

Offers resources to draw social networks with a few clicks on a virtual canvas, load field data from a file in a supported format or crawl the internet to create a social network of connected…

Sentinel…
Desktop

Sentinel Visualizer

Gives a powerful and configurable knowledgebase that makes it easy to store any…

Gives a powerful and configurable knowledgebase that makes it easy to store any information: text, graphics, documents, video, audio, etc. Sentinel Visualizer is a data visualization and analysis…

NodeXL
Desktop

NodeXL Network Overview Discovery and Exploration for Excel

Uses the MSPaint networks. NodeXL Basic is a free, open-source template for…

Uses the MSPaint networks. NodeXL Basic is a free, open-source template for Microsoft Excel 2007, 2010, 2013 and 2016 that makes it easy to explore network graphs. With NodeXL, user can enter a…

NetworKit
Desktop

NetworKit

Provides tools for the analysis of large networks in the size range from…

Provides tools for the analysis of large networks in the size range from thousands to billions of edges. NetworKit is a growing open-source toolkit for large-scale network analysis. It implements…

NetVis Module
Web

NetVis Module

Analyzes and visualizes social networks using data from csv files, online…

Analyzes and visualizes social networks using data from csv files, online surveys, and dispersed teams. The NetVis Module is a free open source web-based tool that gives opportunities to explore…

NetMiner
Desktop

NetMiner

Allows to explore network data visually and interactively. NetMiner is a…

Allows to explore network data visually and interactively. NetMiner is a premium software tool for exploratory analysis and visualization of network data. It can help to detect underlying patterns…

neo4j
Desktop

neo4j

Leverages data relationships as first-class entities, helping enterprises build…

Leverages data relationships as first-class entities, helping enterprises build intelligent applications to meet today’s evolving data challenges. Neo4j is a highly scalable, native graph database.…

JUNG
Desktop

JUNG Java Universal Network/Graph

Provides a common and extendible language for the modelling, analysis, and…

Provides a common and extendible language for the modelling, analysis, and visualization of data that can be represented as a graph or network. JUNG is designed to support a variety of…

JGraphT-sna
Desktop

JGraphT-sna Social Network Analysis addon

Implements several algorithms used in social network analysis (SNA) on top of…

Implements several algorithms used in social network analysis (SNA) on top of the JGraphT library. JGraphT-sna is a Java library for Graphs. It supports generics, where nodes and edges can be of…

InFlow
Desktop

InFlow

Performs social and organizational network analysis and visualization in one…

Performs social and organizational network analysis and visualization in one integrated product. InFlow excels at what-if analysis. It sees how possible network changes may affect work flows,…

GTNA
Desktop

GTNA Graph-Theoretic Network Analyzer

Uses as a graph-theoretic network analysis. GTNA is an efficient Java-based…

Uses as a graph-theoretic network analysis. GTNA is an efficient Java-based toolkit for the comprehensive analysis of complex network graphs. It is simple to extend through a well defined plugin…

GraphStream
Desktop

GraphStream

Helps researchers and developers in their daily tasks of dynamic problem…

Helps researchers and developers in their daily tasks of dynamic problem modelling and of classical graph management tasks: creation, processing, display, etc. GraphStream is a Java-based library…

GraphChi
Desktop

GraphChi

Executes several advanced data mining, graph mining, and machine learning…

Executes several advanced data mining, graph mining, and machine learning algorithms on very large graphs, using just a single consumer-level computer. GraphChi is a disk-based system for computing…

Gephi
Desktop

Gephi

Aims to create a sustainable software and technical ecosystem, driven by a…

Aims to create a sustainable software and technical ecosystem, driven by a large international open-source community, who shares common interests in networks and complex systems. Gephi is a leading…

EgoNet
Desktop

EgoNet Egocentric Network Study Software

A program for the collection and analysis of egocentric social network data.…

A program for the collection and analysis of egocentric social network data. EgoNet helps the user to collect and analyse all the egocentric network data (all social network data of a website on the…

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