Hai Fang
2014-May-21 11:06 UTC
[R] [R-pkgs] Package 'dnet' for omics data integrative analysis
Dear R package developers and users, I am pleased to announce the official release of our newly developed package 'dnet', which intends to analyse omics data in terms of network, evolution and ontology. It has features: 1. Identification of gene-active networks from high-throughput omics data; 2. Network-based sample classifications and visualisations on 2D sample landscape; 3. Random Walk with Restart for network affinity calculation; 4. Semantic similarity between ontology terms (and between their annotated genes); 5. Enrichment analysis using a variety of built-in databases; 6. A wide variety of built-in RData ( http://dnet.r-forge.r-project.org/rdata.html): 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; 7. Support for high-performance parallel computing. For it to be used widely, we have analysed several realcases with step-by-step protocols (http://dnet.r-forge.r-project.org/demos.html). Since it supports many functionalities, we also introduce them individual topics in the form of FAQs (http://dnet.r-forge.r-project.org/faqs.html). Enjoy it! Hai Fang, Ph.D.>From Prof. Gough's Group (http://bioinformatics.bris.ac.uk)Department of Computer Science Univeristy of Bristol Bristol, United Kingdom hfang at cs.bris.ac.uk http://www.cs.bris.ac.uk/~hfang [[alternative HTML version deleted]] _______________________________________________ R-packages mailing list R-packages at r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages