An open-source R package for omics data integrative analysis in terms of network, evolution and ontology

User I/O

Features

  • Identification of gene-active networks from high-throughput omics data (eg expression, mutation and replication timing);
  • Network-based sample classifications and visualisations on 2D sample landscape;
  • Random Walk with Restart for network affinity calculation;
  • Semantic similarity between ontology terms (and between their annotated genes);
  • Enrichment analysis using a variety of built-in databases;
  • A wide variety of built-in RData: ontologies (including Gene Ontology, Disease Ontology, Human Phenotype and Mammalian Phenotype), gene evolutionary age information and gene association networks in well-studied organisms (including human, mouse, rat, chicken, c.elegans, fruitfly, zebrafish and arabidopsis);
  • Support for high-performance parallel computing;
  • A tool with rich visuals but less inputs, which can run on Windows, Mac and Linux.

More

Manual

  • dnet Reference Manual (PDF, HTML)

Demos

URL

Dependency

  • Depends: igraph, supraHex
  • Imports: graph, Rgraphviz, Matrix, Biobase
  • Suggests: limma, survival, foreach, doMC
  • Extends:

License

GPL-2

Author

Hai Fang and Julian Gough