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Network visualization software tools | Biological pathway analysis

Networks are becoming increasingly important to understand the relationships between genotype and phenotype, specifically in the context of disease. Consequently, the demand for efficient network visualization and analysis tools, which can…
VisANT
Web

VisANT

Allows analysis of biological networks. VisANT is a workbench for the…

Allows analysis of biological networks. VisANT is a workbench for the integrative analysis of biological networks, which aims assist network analysis by integrating biological knowledge from…

The Interactome
Web

The Interactome

Visualizes interactions of transcription factors (TFs) in human, mouse and…

Visualizes interactions of transcription factors (TFs) in human, mouse and plant cell types. The Transcription Factor Regulatory Networks browser facilitates the comparison and exploration of…

Pypath
Desktop

Pypath

Offers advanced possibilities for pathway analysis. Pypath builds up networks…

Offers advanced possibilities for pathway analysis. Pypath builds up networks from multiple sources on one igraph object, handles ambiguous ID conversion, reads custom edge and node attributes from…

Cytoscape Web
Desktop

Cytoscape Web

Allows network visualization. Cytoscape Web can be customized and incorporated…

Allows network visualization. Cytoscape Web can be customized and incorporated into any web site. It allows the client application to define a network of nodes and edges and customize their…

BiologicalNetwo…
Desktop

BiologicalNetworks

A research environment for the integral visualization and analysis of…

A research environment for the integral visualization and analysis of heterogeneous biological data. The developed system can be used for the systems-level analysis of host-pathogen interactions,…

NetGestalt
Web

NetGestalt

A web application for integrating multidimensional omics data over biological…

A web application for integrating multidimensional omics data over biological networks. NetGestalt exploits the inherent hierarchical modular architecture of biological networks to achieve high…

ePlant
Web

ePlant

Allows exploration of Arabidopsis thaliana through multiple levels. ePlant…

Allows exploration of Arabidopsis thaliana through multiple levels. ePlant permits researchers to extract information from their data. It can identify connections between layers and facilitate…

CytoCluster
Desktop

CytoCluster

Allows users to identify protein complexes or functional modules. CytoCluster…

Allows users to identify protein complexes or functional modules. CytoCluster is a plugin that integrates several clustering algorithms: (1) BinGO; (2) IPC-MCE; (3) DCU; (4) ClusterONE; (5) IPCA; (6)…

MOSAIC
Desktop

MOSAIC

Performs cell-based layouts using a cell template that defines graphical…

Performs cell-based layouts using a cell template that defines graphical regions. MOSAIC is a Cytoscape plugin to support interactive network annotation and visualization that includes partitioning,…

CellMaps
Web

CellMaps

An HTML5 open-source web tool that allows displaying, editing, exploring and…

An HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed…

PaxtoolsR
Desktop

PaxtoolsR

Enables access to pathway data represented in the BioPAX format and made…

Enables access to pathway data represented in the BioPAX format and made available through the Pathway Commons web service for users of the R language. Features include the extraction, merging, and…

PaVESy
Desktop

PaVESy Pathway Visualization Editing System

Offers the possibility to map profiling data into established knowledge about…

Offers the possibility to map profiling data into established knowledge about biological pathways. PaVESy is a pathway database software that allows to process a whole data set profile in one step.…

WikiPathways
Web

WikiPathways

An open, collaborative platform for capturing and disseminating models of…

An open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. We provide updates on extensions and services to support pathway…

CySBML
Desktop

CySBML Cytoscape Systems Biology Markup Language

Designed to work with Systems Biology Markup Language (SBML) in Cytoscape.…

Designed to work with Systems Biology Markup Language (SBML) in Cytoscape. CySBML includes an importer for BioModels to load SBML from standard repositories. Cytoscape has already been used in…

RadialTopologyV…
Desktop

RadialTopologyViewer

Performs a graphical visualization of a bait protein interactome derived from a…

Performs a graphical visualization of a bait protein interactome derived from a co-immunoprecipitation experiment. RadialTopologyViewer presents the bait as center of the interactome and all…

ProHits-viz
Web

ProHits-viz

Summarizes and displays scored quantitative protein interaction data in…

Summarizes and displays scored quantitative protein interaction data in intuitive ways. ProHits-viz consists of four data analysis and image generation tools complemented by interactive viewers. The…

Pajek
Desktop

Pajek

A program package for analysis and visualization of large networks (having up…

A program package for analysis and visualization of large networks (having up to two billion vertices). Pajek provides tools for analysis and visualization of these networks: collaboration networks,…

LogMiNeR
Desktop

LogMiNeR Logistic Multiple Network-constrained Regression

Studies classification-based investigations that leads to increased biological…

Studies classification-based investigations that leads to increased biological interpretability. LogMiNeR was applied to transcriptional profiling data to better understand differential influenza…

NAIL
Desktop

NAIL Network Analysis and Inference Library

A set of software tools to simplify the range of computational activities…

A set of software tools to simplify the range of computational activities involved in regulatory network inference. NAIL is technology-independent and includes an interface layer to allow easy…

Ondex
Desktop
Web

Ondex

Allows to link, integrate and visualize through graph analysis techniques data…

Allows to link, integrate and visualize through graph analysis techniques data from diverse biological data sets. ONDEX combines large-scale database integration, sequence analysis, text mining,…

GLay
Desktop

GLay

Offers a collection of algorithms and graph layout functions for network…

Offers a collection of algorithms and graph layout functions for network clustering and structured visualization. GLay is particularly useful for decomposition, display and exploratory analysis of…

STON
Desktop

STON SBGN TO Neo4j

A graph-based tool to extend the existing infrastructure for storing and…

A graph-based tool to extend the existing infrastructure for storing and exploring biological pathways in Systems Biology Graphical Notation-Markup Language (SBGN-ML) format. STON can transform SBGN…

CompNet
Desktop

CompNet

Allows simultaneous visualization and comparison of multiple networks. In…

Allows simultaneous visualization and comparison of multiple networks. In addition to computing generic graph properties for individual networks, CompNet allows multigraph comparisons and similarity…

RedeR
Desktop

RedeR

Provides a comprehensive and entirely framework to read, write and manipulate R…

Provides a comprehensive and entirely framework to read, write and manipulate R code mixed to a Java data structure. RedeR is designed for the representation of nested and hierarchical biological…

CyToStruct
Desktop

CyToStruct

A transparent interface between the Cytoscape platform for network analysis and…

A transparent interface between the Cytoscape platform for network analysis and molecular viewers, including PyMOL, UCSF Chimera, VMD, and Jmol. CyToStruct launches and passes scripts to molecular…

GRNsight
Web

GRNsight

A web application and service for visualizing models of gene regulatory…

A web application and service for visualizing models of gene regulatory networks (genes, transcriptions factors and the regulatory connexions between them). GRNsight provides an easy way to visualize…

ChiBE
Desktop

ChiBE Chisio BioPAX Editor

Allows users to tap into the detailed pathway information corpus for genomic…

Allows users to tap into the detailed pathway information corpus for genomic data analysis. This would not be possible without its three key features: process views, specialized graph queries, and…

BNOmics
Desktop

BNOmics Bayesian Network Omics

Infers and analyzes Bayesian Networks from omics datasets. BNOmics aims at…

Infers and analyzes Bayesian Networks from omics datasets. BNOmics aims at comprehensive systems biology—type data exploration, including both generating new biological hypothesis and testing and…

WebInterViewer
Desktop

WebInterViewer

Analyzes the interactions from any system. WebInterViewer is a web-based…

Analyzes the interactions from any system. WebInterViewer is a web-based application program that produces a molecular interaction network of good quality without computing force between every pair…

PiiL
Desktop

PiiL Pathway interactive visualization tooL

Allows direct comparison and testing specific hypotheses in model organisms for…

Allows direct comparison and testing specific hypotheses in model organisms for which pathway and expression network data exists. PiiL is an integrated DNAm and expression pathway browser. It was…

GraphWeb
Web

GraphWeb

Allows for biological network analysis and module discovery. GraphWeb provides…

Allows for biological network analysis and module discovery. GraphWeb provides methods to: (i) integrate heterogeneous and multispecies data for constructing directed and undirected, weighted and…

CellWhere
Web

CellWhere

Produces an interactive graphical display that mimics the structure of a cell,…

Produces an interactive graphical display that mimics the structure of a cell, showing the local interaction network organized into subcellular locations. This user-friendly tool helps in the…

CL
Web

CL Cancer Landscapes

Provides data-derived statistical network models for 8 human cancers. CL…

Provides data-derived statistical network models for 8 human cancers. CL contains several functions for biological interpretability of the network models, such as pathway analysis, drug-target…

NaviCell
Web

NaviCell

A tool for network-based visualization of ‘omics’ data which implements several…

A tool for network-based visualization of ‘omics’ data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and…

PathWhiz
Web

PathWhiz

A web server designed to create colourful, visually pleasing and biologically…

A web server designed to create colourful, visually pleasing and biologically accurate pathway diagrams that are both machine-readable and interactive. As a web server, PathWhiz is accessible from…

NaviCom
Web

NaviCom

A web application for visualization of multi-level omics data on top of…

A web application for visualization of multi-level omics data on top of biological network maps. NaviCom uses a large datasets from omics data resources to displaying them on a molecular network maps…

D-Map
Web

D-Map

A web application capable of generating and manipulating advanced differential…

A web application capable of generating and manipulating advanced differential networks by combining state-of-the-art inference reconstruction methods with random walk simulations. With D-Map,…

iCAVE
Desktop

iCAVE interactome-CAVE

Provides a platform for visualizing complex biomolecular interaction networks.…

Provides a platform for visualizing complex biomolecular interaction networks. iCAVE is an open-source software that authorizes to picture large and complex networks in 3D, stereoscopic 3D or…

ViSiBooL
Desktop

ViSiBooL Visualization and Simulation of Boolean networks

A tool for GUI-based modeling of Boolean Networks. ViSiBooL supports an…

A tool for GUI-based modeling of Boolean Networks. ViSiBooL supports an extended version of synchronous Boolean Networks with temporal predicates. ViSiBooL allows user-friendly modeling, organization…

VISUALGRAPHX
Web

VISUALGRAPHX

A web-based, interactive visualization tool for large-scale graphs.…

A web-based, interactive visualization tool for large-scale graphs. VisualGraphX aims to provide a universal graph visualization tool that empowers the users to efficiently explore the data for…

DyNet
Desktop

DyNet

A Cytoscape plug-in that visualizes differences among multiple networks. DyNet…

A Cytoscape plug-in that visualizes differences among multiple networks. DyNet can be used for analysing how networks change over time or across multiple conditions (dynamic networks). DyNet utilizes…

Cytoscape.js
Desktop

Cytoscape.js

An open-source JavaScript-based graph library. Its most common use case is as a…

An open-source JavaScript-based graph library. Its most common use case is as a visualization software component, so it can be used to render interactive graphs in a web browser. It also can be used…

Medusa
Desktop

Medusa

A java standalone application for visualization and clustering analysis of…

A java standalone application for visualization and clustering analysis of biological networks in 2D. Medusa is highly interactive and it supports weighted and multi-edged graphs where each edge…

NetBioV
Desktop

NetBioV Network Biology Visualization

Allows the efficient visualization of large biological networks by emphasizing…

Allows the efficient visualization of large biological networks by emphasizing important aspects of biological information processing. NetBioV provides four principle types of layout styles: global,…

MacSyView
Desktop

MacSyView Macromolecular System Viewer

Offers a graphical user interface (GUI) to simplify analysis of results of…

Offers a graphical user interface (GUI) to simplify analysis of results of MacSyFinder. MacSyView displays overviews of component content and genomic context. It returns views of detected systems in…

Orthoscape
Desktop

Orthoscape

Analyzes evolutionary information in the gene sets and networks. Orthoscape is…

Analyzes evolutionary information in the gene sets and networks. Orthoscape is a Cytoscape module that allows to search for homologs (orthologs and/or paralogs) and to perform phylostratigraphic…

PathVisioRPC
Desktop

PathVisioRPC

An XML-RPC interface for the pathway analysis tool PathVisio. PathVisioRPC…

An XML-RPC interface for the pathway analysis tool PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting…

DeDaL
Desktop

DeDaL Data-Driven Network Layouting

Allows constructing biological network layouts based on the data from molecular…

Allows constructing biological network layouts based on the data from molecular profiles imported as values of node attributes. DeDaL is a Cytoscape 3 app, which uses linear and non-linear algorithms…

BioPAX…
Desktop

BioPAX translator

Allows users to create pathway diagrams using CellDesigner and save the data…

Allows users to create pathway diagrams using CellDesigner and save the data accurately in BioPAX format. The BioPAX translator is implemented as a CellDesigner plug-in, so that timely updates can be…

BIANA
Desktop

BIANA Biologic Interaction and Network Analysis

A tool for biological information integration and network management. BIANA is…

A tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological…

PathVisio
Desktop

PathVisio

A free open-source pathway analysis and drawing software. PathVisio allows you…

A free open-source pathway analysis and drawing software. PathVisio allows you to draw, edit and analyse biological pathways. You can visualize your own experimental data on the pathways and find…

ArrayXPath
Web

ArrayXPath

A web-based service for mapping and visualizing microarray gene-expression data…

A web-based service for mapping and visualizing microarray gene-expression data for integrated biological pathway resources using Scalable Vector Graphics (SVG). By integrating major bio-databases…

FuncTree
Web

FuncTree

Maps omics data onto a predefined circular dendrogram called the “Functional…

Maps omics data onto a predefined circular dendrogram called the “Functional Tree map”. FuncTree allows user to overview the broad functionality of their data, for a more accurate and comprehensive…

COMICS
Web

COMICS

Allows combined integration and visualization of molecular expression data in…

Allows combined integration and visualization of molecular expression data in some vertebrate model organisms. COMICS employs pre-existing anatomical ontologies to map arbitrary omics data across…

TPV
Desktop

TPV Temporal Pathway Visualizer

Offers a visualization tool for network and time series data. TPV is mainly…

Offers a visualization tool for network and time series data. TPV is mainly suited for supporting results from the TPS software. It is able to assemble temporal phosphoproteomic data into signalling…

visJS2jupyter
Desktop

visJS2jupyter

Produces interactive networks. visJS2jupyter provides options to export…

Produces interactive networks. visJS2jupyter provides options to export networks for further analysis and biological interpretation in Cytoscape. It brings the processes of building, interacting with…

TROVE
Desktop

TROVE NeTwork-based hallmaRk annOtation, Visualization and charactErization

Facilitates the study of cancer signaling networks from the hallmark…

Facilitates the study of cancer signaling networks from the hallmark perspective. TROVE provides an integrated platform that allows construction of a specific cancer signaling network, assists users…

BioPAXViz
Desktop

BioPAXViz

Provides a robust and user-friendly interface for visual analysis of multiple…

Provides a robust and user-friendly interface for visual analysis of multiple pathways in a comparative genomics context. BioPAXViz is a lightweight pathway visualizer implemented as a Cytoscape…

Pathview Web
Web

Pathview Web

Serves for pathway-based visualization and data integration. Pathview Web…

Serves for pathway-based visualization and data integration. Pathview Web provides both graphical user interface (GUI) and application programming interface (API) to Pathview. The interactive…

NET
Desktop

NET Network Extraction Tool

Provides fast and efficient means for the processing and quantification of…

Provides fast and efficient means for the processing and quantification of biological networks like Drosophila tracheoles or leaf venation patterns. NET is designed for high-throughput semi-automated…

LibSBGN
Desktop

LibSBGN

Provides a software library for reading, writing and manipulating Systems…

Provides a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. LibSBGN makes it easy for…

ppiData
Desktop

ppiData

Contains the directed graphs for protein interaction data as derived from Y2H…

Contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository. ppiData is developed as an explicit…

structureViz
Desktop

structureViz

Links the visualization of biological networks provided by Cytoscape with the…

Links the visualization of biological networks provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera. structureViz is a…

Arcadia
Desktop

Arcadia

Translates text-based descriptions of biological networks into standardized…

Translates text-based descriptions of biological networks into standardized diagrams. The data structure can be decomposed into three interconnected layers: (i) the first one corresponds to the data…

VistaClara
Desktop

VistaClara

Visualizes gene and protein expression within a network context. VistaClara…

Visualizes gene and protein expression within a network context. VistaClara extends the traditional heat map views into dynamic interactive permutation, and allows users to incorporate meta-data…

GenePro
Desktop

GenePro

Provides several integrative and interactive visualization and analysis tools…

Provides several integrative and interactive visualization and analysis tools for protein-protein interaction (PPI) networks. Unlike VisANT, we use a cluster-centric top-down approach. Given a PPI…

KEGGgraph
Desktop

KEGGgraph

A software package in R and Bioconductor, an interface between KEGG pathways…

A software package in R and Bioconductor, an interface between KEGG pathways and graph models as well as a collection of tools for these graphs. Superior to existing approaches, KEGGgraph captures…

linkcomm
Desktop

linkcomm

Provides a set of tools for generating, visualizing, and analysing link…

Provides a set of tools for generating, visualizing, and analysing link communities in networks of arbitrary size and type. The linkcomm package also includes tools for generating, visualizing, and…

Hyperscape
Web

Hyperscape

A hypergraph implementation that better captures hierarchical structures, using…

A hypergraph implementation that better captures hierarchical structures, using components of elastic fibers and, chromatin modification as models. These reveal unprecedented views of the biology of…

G T A T C G C T A
BioJS
Desktop

BioJS

An open-source project whose main objective is the visualization of biological…

An open-source project whose main objective is the visualization of biological data in JavaScript. BioJS provides an easy-to-use consistent framework for bioinformatics application programmers. It…

Pathview
Desktop

Pathview

Provides pathway based data integration and visualization. Pathview maps and…

Provides pathway based data integration and visualization. Pathview maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify…

rBiopaxParser
Desktop

rBiopaxParser

Provides a comprehensive set of functions for parsing, viewing and modifying…

Provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. These functions enable the user to access and modify specific parts of the BioPAX model.…

G T A T C G C T A
MicroScope
Web
Desktop

MicroScope

A ChIP-seq and RNA-seq software suite for visualizing and analyzing genomic…

A ChIP-seq and RNA-seq software suite for visualizing and analyzing genomic data, including features to support differential expression analysis, heatmap production, principal component, gene…

eXamine
Desktop

eXamine

A set-oriented visual analysis approach for annotated modules that displays set…

A set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. eXamine extends upon Self Organizing Maps to simultaneously lay…

Cytoscape
Desktop

Cytoscape

An open source software platform for visualizing molecular interaction networks…

An open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.…

Escher
Web

Escher

A web-based tool for building, viewing, and sharing visualizations of…

A web-based tool for building, viewing, and sharing visualizations of biological pathways. These 'pathway maps' are a great way to contextualize data about metabolism. Three key features…

MarVis-Pathway
Desktop

MarVis-Pathway Marker Visualization Pathway

Allows the user to identify metabolites by annotation of pathways from…

Allows the user to identify metabolites by annotation of pathways from cross-omics data. The analysis is supported by an extensive framework for pathway enrichment and meta-analysis. MarVis-Pathway…

BioLayout…
Desktop

BioLayout Express(3D)

A powerful tool for the visualization and analysis of network graphs.…

A powerful tool for the visualization and analysis of network graphs. Network-based approaches are becoming increasingly popular for the analysis of complex systems of interaction and high…

Collective…
Desktop

Collective Analysis of Biological Interaction Networks

Provides tools for visualizing and analyzing interactions data from multiple…

Provides tools for visualizing and analyzing interactions data from multiple sources of evidence. CABIN is an open source network visualization and analysis tool which promotes analytical reasoning…

DomainGraph
Desktop

DomainGraph

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

A Java plugin for Cytoscape, a software platform for the analysis and visualization of molecular interaction networks. The main functionality of the DomainGraph plugin is the visual analysis of the…

MIM notation
Terminology

MIM notation Molecular Interaction Maps notation

Provides a list of convention for annotating and organize relationships in…

Provides a list of convention for annotating and organize relationships in bioregulatory systems. MIM notation describes the relationships between multiple entities by using interactions glyphs, a…

cy3sabiork
Desktop

cy3sabiork

Queries and visualizes kinetic data from SABIO-RK in Cytoscape. cy3sabiork…

Queries and visualizes kinetic data from SABIO-RK in Cytoscape. cy3sabiork creates an intuitive visualization of kinetic entries in form of a species-reaction-kinetics graph, which reflects the…

PIANA
Desktop

PIANA Protein Interactions And Network Analysis

Facilitates working with protein interaction networks by (1) integrating data…

Facilitates working with protein interaction networks by (1) integrating data from multiple sources, (2) providing a library that handles graph-related tasks and (3) automating the analysis of…

KUPNetViz
Web

KUPNetViz Kidney and Urinary Pathway Network Visualizer

A biological graph exploration tool allowing the exploration of Kidney &…

A biological graph exploration tool allowing the exploration of Kidney & Urinary Pathway Knowledge Base (KUPKB) data through the visualization of biomolecule interactions. KUPNetViz provides…

clusterMaker
Desktop

clusterMaker

Implements several clustering algorithms and provides network, dendrogram, and…

Implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. ClusterMaker provides a number of clustering algorithms and visualizations that can be…

3DScapeCS
Desktop

3DScapeCS

A Cytoscape plugin providing three-dimensional, dynamic, parallel network…

A Cytoscape plugin providing three-dimensional, dynamic, parallel network visualization for Cytoscape in client–server (C/S) architecture. The 3D perspective not only guarantees user a greater…

Mimoza
Desktop
Web

Mimoza

A metabolic model visualization and navigation system that allows for…

A metabolic model visualization and navigation system that allows for exploration of metabolic models in a semantically zoomable manner. The most general view represents the compartments of the…

SNAVI
Desktop

SNAVI Signaling Networks Analysis and VIsualization

A Windows-based desktop application that implements standard network analysis…

A Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means…

NaviCluster
Desktop

NaviCluster

Provides interactive and multi-scale network navigation to a wide range of…

Provides interactive and multi-scale network navigation to a wide range of biologists in the big data era, via the de facto standard platform for network visualization. The underlying components of…

BiNA
Desktop

BiNA Biological Network Analyzer

A workbench for visualizing and analyzing biological networks. Highly…

A workbench for visualizing and analyzing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation…

MIMTool
Desktop

MIMTool Molecular Interaction Maps Tool

Allows users to build Molecular Interaction Maps diagrams according to MIM…

Allows users to build Molecular Interaction Maps diagrams according to MIM notation. MIMTool provides a graphic interface divided into three mains components: (i) a drawing tool related to a toolbox…

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…

EPE
Desktop

EPE Edinburgh Pathway Editor

Allows to draw and manipulate Biological Networks, such as signalling or…

Allows to draw and manipulate Biological Networks, such as signalling or metabolic pathways. EPE is a biological pathway that can draw diagrams using SBGN PD Level 1, Cytoscape and Metabolic…

Systrip
Desktop

Systrip

Provides a visualization tool for biological network. Systrip provides several…

Provides a visualization tool for biological network. Systrip provides several metabolic network representations including time-series and 3D molecular systems. The software authorizes network and…

ONCO.IO
Web

ONCO.IO

Explores complex gene regulatory system involved in cancer. ONCO.IO is an…

Explores complex gene regulatory system involved in cancer. ONCO.IO is an integrative resource for micro RNA and transcription factors analysis in cancer. This method provides network analysis tools…

visNetwork
Desktop

visNetwork

Provides an R package for network visualization, using vis.js javascript…

Provides an R package for network visualization, using vis.js javascript library. visNetwork allows an interactive visualization of networks. The package proposes all the features available in vis.js…

Director
Desktop

Director

Streamlines the visualization of molecular effects in regulatory cascades.…

Streamlines the visualization of molecular effects in regulatory cascades. Director is an R package designed to provide a fast and easy, browser-enabled solution to discovering potentially…

Clust&See
Desktop

Clust&See

Identifies, visualizes and analyses clusters from large networks. Clust&See…

Identifies, visualizes and analyses clusters from large networks. Clust&See provides three different, recently developed graph clustering algorithms, one of which can produce overlapping…

SAFE
Desktop

SAFE Spatial Analysis for Functional Enrichment

Allows users to generate comprehensive functional maps of networks. SAFE maps…

Allows users to generate comprehensive functional maps of networks. SAFE maps local over/under-representation of functional attributes. It performs local enrichment analysis to determine which…

EntOptLayout
Desktop

EntOptLayout

Implements a graph layout/network visualization algorithm using a recently…

Implements a graph layout/network visualization algorithm using a recently published relative entropy optimization based method. EntOptLayout allows to visualize a weighted network.

CytoKegg
Desktop

CytoKegg

Searches and imports KEGG pathways to Cytoscape. In addition, Cytokegg can find…

Searches and imports KEGG pathways to Cytoscape. In addition, Cytokegg can find KEGG pathways in a given network. Once there select the net.

CyAnimator
Desktop

CyAnimator

Creates simple animations of Cytoscape networks. CyAnimator allows the user to…

Creates simple animations of Cytoscape networks. CyAnimator allows the user to take a series of snapshots (called frames) of Cytoscape networks. It can animate two frames between them by…

CerebralWeb
Desktop

CerebralWeb

Enables the fast and interactive visualization of molecular interaction…

Enables the fast and interactive visualization of molecular interaction networks stratified based on subcellular localization or other user-supplied annotation and is designed to be easily integrated…

KENeV
Web

KENeV KEGG Enriched Network Visualizer

An online web application which enables a fully automated workflow starting…

An online web application which enables a fully automated workflow starting from a list of differentially expressed genes and deriving the enriched KEGG metabolic and signaling pathways, merged into…

ZoomOut
Web

ZoomOut

A tool for analysis, visualization and clustering of networks as a super…

A tool for analysis, visualization and clustering of networks as a super network, based on their calculated feature properties. Networks can be analysed and be further treated as single nodes in a…

PathwayMatrix
Desktop

PathwayMatrix

Presents an alternative visual representation of biological pathways using an…

Presents an alternative visual representation of biological pathways using an interactive matrix representation instead of a node-linked diagram. PathwayMatrix supports interactive capabilities to…

KEGGanim
Web

KEGGanim

Provides a web-based tool for visualizing experimental data in biological…

Provides a web-based tool for visualizing experimental data in biological pathways. KEGGanim produces animations and images of KEGG pathways using public or user uploaded high-throughput data.…

VitaPad
Desktop

VitaPad

Uses to visualize biological pathways and map experimental data to them.…

Uses to visualize biological pathways and map experimental data to them. VitaPad is a cross-platform application that enables users to create and modify biological pathway diagrams and incorporate…

GALANT
Desktop

GALANT GrAph LANdscape VisualizaTion

Builds functional landscapes onto biological networks. GALANT, makes possible…

Builds functional landscapes onto biological networks. GALANT, makes possible to project any type of numerical data onto a network to create a smoothed data map resembling the network layout. For…

KEGGParser
Desktop

KEGGParser KEGG Pathway semiautomatic parser/editor

A MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing,…

A MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. KEGGParser, in addition to providing all the functionality available in…

Biographer
Web

Biographer

A web-based renderer and editor for reaction networks, which can be integrated…

A web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Biographer enables visualizations based on the…

GOlorize
Desktop

GOlorize

Provides class-guided network visualization in Cytoscape. GOlorize uses Gene…

Provides class-guided network visualization in Cytoscape. GOlorize uses Gene Ontology (GO) categories or other additional class information to direct the network graph layout process and to emphasize…

PIVOT
Desktop

PIVOT Protein Interactions VisualizatiOn Tool

A Java-based tool, for visualizing protein-protein interactions. PIVOT is rich…

A Java-based tool, for visualizing protein-protein interactions. PIVOT is rich in features that help the users navigate and interpret the interactions map, as well as graph-theory algorithms for…

N2C
Web

N2C Network2Canvas

A web application that provides an alternative way to view networks. N2C…

A web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas. The network nodes are clustered on the canvas using…

Pathways…
Desktop

Pathways Database System

A set of software tools for modeling, storing, analyzing, visualizing, and…

A set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail. The features…

NAViGaTOR
Desktop

NAViGaTOR Network Analysis, Visualization, & Graphing TORonto

A powerful graphing application for the 2D and 3D visualization of biological…

A powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable…

PINV
Desktop
Web

PINV Protein Interaction Network Visualizer

An open source, native web application that facilitates the visualization of…

An open source, native web application that facilitates the visualization of protein interactions. PINV provides an attractive view of complex, fully interactive networks with components that allow…

VANTED
Desktop

VANTED Visualization and Analysis of Networks containing Experimental Data

A framework for systems biology applications, which comprises a comprehensive…

A framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconstruction, data visualization, integration of various data types,…

MarVis-Graph
Desktop

MarVis-Graph

A software tool for integrative analysis of metabolic and transcriptomic data.…

A software tool for integrative analysis of metabolic and transcriptomic data. All experimental data is investigated in terms of the full metabolic network obtained from a reference database. The…