NetPathMiner

NetPathMiner is a framework designed for extracting and analyzing paths related to specific experimental conditions from genome-scale networks. This tool accommodates a variety of input formats, including KGML, SBML, and BioPAX files, and offers the flexibility to work with networks in metabolic, reaction, and gene representations. By ranking paths extracted from these networks, NetPathMiner facilitates interpreting complex data by applying Markov model-based clustering and classification techniques.

A key feature of NetPathMiner is its focus on user-friendly analysis, providing static and interactive visualizations of networks and paths. This feature is handy for manual investigations, allowing researchers to explore the intricate details of the paths relevant to their studies.

Topic

Molecular interactions, pathways and networks;Machine learning;Endocrinology and metabolism;Gene expression

Detail

  • Operation: Network simulation

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: GNU General Public License, version 2

  • Cost: Free

  • Version name: 1.38.0

  • Credit: KAKENHI of MEXT, Japan.

  • Input: -

  • Output: -

  • Contact: Ahmed Mohamed mohamed@kuicr.kyoto-u.ac.jp

  • Collection: -

  • Maturity: Stable

Publications

  • NetPathMiner: R/Bioconductor package for network path mining through gene expression.
  • Mohamed A, et al. NetPathMiner: R/Bioconductor package for network path mining through gene expression. NetPathMiner: R/Bioconductor package for network path mining through gene expression. 2014; 30:3139-41. doi: 10.1093/bioinformatics/btu501
  • https://doi.org/10.1093/bioinformatics/btu501
  • PMID: 25075120
  • PMC: PMC4609018

Download and documentation

< Back to DB search