Network visualization software tools | Shotgun metagenomic sequencing data 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 interoperate with modern data analysis environments, such as the web, is increasing in parallel.
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 different sources or layers of complexity. The software provides exploratory navigation to walk through the interactions and metagraph capability for multi-scale visualization with integrated context information.
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 transcription factor interactions between a variety of cell types. Interaction, genes and cell types can be selected, as well as export network graphs to text and SVG for downstream analysis and editing.
Records common knowledge represented in biological pathways. WikiPathways is a collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. It was developed to biological pathways, facilitating the contribution and maintenance of pathway information from the scientific community. This online database is improved by continuous data curation.
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 the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.
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. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.
Serves for association indices and clustering. GAIN employs a user-selected association index followed by hierarchical clustering and by displaying a heatmap to calculate all pair-wise values. It can estimate if an association index can discriminate the interaction profile similarity of a particular set of node pairs of interest from all node pairs. This tool can be employed in a gene regulatory network.
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 text files and MySQL. Pypath automatically updates its content, which is dynamically gathered from resources. It is also capable of compiling networks from custom sets of interaction resources and can integrate additional annotations.
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 analysis tools can (i) cluster baits and prey for dot plot images, (ii) perform correlation analysis, (iii) calculate prey specificity scores and, (iv) generate detailed bait–bait comparisons. This method enables visualization of the results from the dot plot and correlation tools directly in the browser.
Enables users to compare the global and local biological signal of networks. GeNets takes into consideration signal-to-noise ratio, coverage, density, and unique topology. It allows users to visualize, store, manage, and share pathway analyzes. Moreover, this tool intends to permit users to test any network they choose by training network-specific Quack models.
A web application for integrating multidimensional omics data over biological networks. NetGestalt exploits the inherent hierarchical modular architecture of biological networks to achieve high scalability. In contrast with typical network visualization tools, NetGestalt allows multiscale representation and navigation of the data, and it adjusts graphical presentations to the level of detail appropriate to a particular scale. It also allows simultaneous visualization of different types of data within the same framework to facilitate data integration.
Allows simultaneous visualization and comparison of multiple networks. In addition to computing generic graph properties for individual networks, CompNet allows multigraph comparisons and similarity based grouping of networks. It also allows visual identification and selection of sub-graphs/communities of interest, enabling a general user to work with and compare between sufficiently complex and large networks. CompNet is a valuable tool for biologists and other researchers working in the field of visual data mining.
Informs on semantic zooming principles for map navigation and assists users to explore comprehensive molecular maps similar to geographical maps. NaviCell is a web application dedicated to the study of large maps of molecular interactions created by the group of computational systems biology of cancer at Institut Curie. This tool includes four main features: (1) data visualization; (2) web blog for collecting community feedback; (3) semantic zoom for viewing different levels of details on the map; and (4) map browsing by Google™ Map engine.
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 dimensional data. Networks can be produced from a wide variety of relationships between entities. In biology this includes the interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, etc. GraphiaPro has been specifically designed for visualization, clustering, exploration and analysis of very large network graphs in two- and three-dimensional space derived primarily, but not exclusively, from biological 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 and searching pathway resources, ArrayXPath automatically maps different types of identifiers from microarray probes and pathway elements. When one inputs gene-expression clusters, ArrayXPath produces a list of the best matching pathways for each cluster.
Handles systems biology graphical notation (SBGN) maps. SBGN-ED is an additional module to the VANTED software with the aim of facilitating the analysis and visualization of biological networks. It offers features for (i) generating SBGN maps; (ii) editing SBGN map; (iii) syntactic and semantic validating of SBGN maps; (iv) automatically translating of networks from KEGG and MetaCrop software to SBGN format; (v) and exporting maps in various formats.
Serves for the analysis of human data. 3Omics simplifies the data analysis by combining the advantages and operations of several existing systems and packages into a single platform. It accepts multiple experimental conditions or time-dependent transcriptomics data, proteomics data or metabolomics data. Users can perform correlation analysis, coexpression profiling, phenotype mapping, pathway enrichment analysis and Gene Ontology (GO) enrichment analysis.
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 between two bioentities can represent a different biological concept. Comparing to previous versions, it is currently enriched with a variety of layout and clustering methods for more intuitive visualizations. It is easy to integrate with web application since it is offered as an applet.
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, graph analysis and allows users to visualize the data. The software can handle very large graphs and represent many hundreds of thousands of data items. It can be used for analysis and interpretation of experimental results.
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 protein-protein interaction networks. PIANA can also be used as a stand-alone application to create protein interaction networks and perform tasks such as predicting protein interactions and helping to identify spots in a 2D electrophoresis gel.