Encore: Genetic Association Interaction Network centrality pipeline and application to SLE exome data.

ABSTRACT: Open source tools are needed to facilitate the construction, analysis, and visualization of gene-gene interaction networks for sequencing data. To address this need, we present Encore, an open source network analysis pipeline for genome-wide association studies and rare variant data. Encore constructs Genetic Association Interaction Networks or epistasis networks using two optional approaches: our previous information-theory method or a generalized linear model approach. Additionally, Encore includes multiple data filtering options, including Random Forest/Random Jungle for main effect enrichment and Evaporative Cooling and Relief-F filters for enrichment of interaction effects. Encore implements SNPrank network centrality for identifying susceptibility hubs (nodes containing a large amoun

SUBMITTER: Davis NA 

PROVIDER: S-EPMC3955726 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature