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 (e.g. mutation, expression, 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

• Poster in ISMB2014