title: NetPathMiner: R/Bioconductor package for network path mining through gene expression.
abstract: 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.
  
  
  BACKGROUND
  The package is available through Bioconductor and from Github at http://github.com/ahmohamed/NetPathMiner.
authors: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia.
authors: Ahmed
authors: A
authors: Mohamed
authors: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia.
authors: Timothy
authors: T
authors: Hancock
authors: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia.
authors: Canh Hao
authors: CH
authors: Nguyen
authors: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Japan and Department of Computing and Information Systems, The University of Melbourne, Victoria, Australia.
authors: Hiroshi
authors: H
authors: Mamitsuka
mesh_terms: D050260:Carbohydrate Metabolism / Q000235:genetics; D016000:Cluster Analysis; D003196:Computer Graphics; D057225:Data Mining / Q000379:methods*; D023281:Genomics; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics*; D012984:Software; D059467:Transcriptome