NetPathMiner: R/Bioconductor package for network path mining through gene expression.
Ontology highlight
ABSTRACT: Unlabelled
NetPathMiner is a general framework for mining, from genome-scale networks, paths that are related to specific experimental conditions. NetPathMiner interfaces with various input formats including KGML, SBML and BioPAX files and allows for manipulation of networks in three different forms: metabolic, reaction and gene representations. NetPathMiner ranks the obtained paths and applies Markov model-based clustering and classification methods to the ranked paths for easy interpretation. NetPathMiner also provides static and interactive visualizations of networks and paths to aid manual investigation.Availability
The package is available through Bioconductor and from Github at http://github.com/ahmohamed/NetPathMiner.
SUBMITTER: Mohamed A
PROVIDER: S-EPMC4609018 | biostudies-literature | 2014 Nov
REPOSITORIES: biostudies-literature
Publications
NetPathMiner: R/Bioconductor package for network path mining through gene expression.
Mohamed Ahmed A Hancock Timothy T Nguyen Canh Hao CH Mamitsuka Hiroshi H
Bioinformatics (Oxford, England) 20140728 21
<h4>Unlabelled</h4>NetPathMiner is a general framework for mining, from genome-scale networks, paths that are related to specific experimental conditions. NetPathMiner interfaces with various input formats including KGML, SBML and BioPAX files and allows for manipulation of networks in three different forms: metabolic, reaction and gene representations. NetPathMiner ranks the obtained paths and applies Markov model-based clustering and classification methods to the ranked paths for easy interpre ...[more]
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