EGAD: ultra-fast functional analysis of gene networks

• DOI: 10.1093/bioinformatics/btw695
• Publication Date: 2016-11-03T20:06:46Z
• Authors: Sara Ballouz; Melanie Weber; Paul Pavlidis; Jesse Gillis
• Keywords: Bioconductor; R package; Gene regulatory network; MIT License; Network Analysis

Evaluating gene networks with respect to known biology is a common task but often computationally costly one. Many computational experiments are difficult apply exhaustively in network analysis due run-times. To permit high-throughput of networks, we have implemented set very efficient tools calculate functional properties based on guilt-by-association methods. ( xtending ' uilt-by- ssociation' by egree) allows be evaluated hundreds or thousands sets. The methods predict novel members groups, assess how well groups sets genes, and determines the degree which generic predictions drive performance. By allowing fast evaluations, whether random real ones, provides user an assessment performance can easily used controlled evaluations across many parameters.The software package freely available at https://github.com/sarbal/EGAD for use R Matlab. also under LGPL license from Bioconductor web site http://bioconductor.org )[e-mail] data Bioinformatics online.