Table 7.
Software libraries and tools for biological network analysis
| Name | Description | URL |
|---|---|---|
| Bio4J | Bio4j is a bioinformatics graph-based database | http://www.bio4j.com/ |
| BioConductor (Graphs and Networks view) | Collection of BioConductor modules for biological network analysis and visualization | http://www.bioconductor.org/packages/release/BiocViews.html#___GraphsAndNetworks |
| Cytoscape | Open source platform for complex network analysis and visualization with a large collection of plug-ins for biological network analysis | http://www.cytoscape.org/ |
| DAVID | Integrated functional annotation tool | http://david.abcc.ncifcrf.gov/home.jsp |
| FunDO | Functional Disease Ontology server | http://django.nubic.northwestern.edu/fundo/ |
| gene2pathway | R package for prediction of KEGG pathway membership for individual genes based on InterPro domain signatures | http://www.bioconductor.org/packages/release/bioc/html/gene2pathway.html |
| GeneAnswers | R package for biological or medical interpretation of the given one or more groups of genes by means of statistical test | http://www.bioconductor.org/packages/release/bioc/html/GeneAnswers.html |
| GO Tools | Tools for analysis of GO T term enrichment, statistical analysis, semantic similarity and functional similarity using GO terms derived from gene lists | http://www.geneontology.org/GO.tools.shtml |
| Gephi | Open-source graph visualization and analysis software | http://www.gephi.org |
| Gremlin | Graph-based programming language | https://github.com/tinkerpop/gremlin/wiki/ |
| iGraph | Network analysis and visualization library in C. Also available R package and a Python extension | http://igraph.sourceforge.net/ |
| KEGGgraph | R package for analysis of KEGG pathways | http://www.bioconductor.org/packages/2.10/bioc/html/KEGGgraph.html |
| LEDA | A broad-spectrum C++ class library for efficient data types and algorithms including large-scale network analysis | http://www.algorithmic-solutions.com/leda/about/index.htm |
| Neat | Web-based network analysis tools | http://gephi.org/ |
| Ontology Analysis plugins for Cytoscape | http://chianti.ucsd.edu/cyto_web/plugins/ | Plugins for functional enrichment analysis using network data |
| PANTHER | Classification of genes and proteins | http://pantherdb.org/ |
| Reactome | Curated knowledgebase of molecular events and pathways | http://www.reactome.org |
| TargetMine | Integrates different types of biological data and enable flexible queries, export results and analyze lists of data. | http://targetmine.mizuguchilab.org |