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NetPathMiner for Biological Network Construction, Path Mining and Visualization

Bioconductor version: Release (3.19)

NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.

Author: Ahmed Mohamed [aut, cre] , Tim Hancock [aut], Tim Hancock [aut]

Maintainer: Ahmed Mohamed <mohamed at>

Citation (from within R, enter citation("NetPathMiner")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

NetPathMiner Vignette HTML R Script
Reference Manual PDF


biocViews Classification, Clustering, GraphAndNetwork, Network, Pathways, Software
Version 1.40.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL (>= 2)
Depends R (>= 3.0.2), igraph (>= 1.0)
System Requirements libxml2, libSBML (>= 5.5)
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Suggests rBiopaxParser(>= 2.1), RCurl, graph, knitr, rmarkdown, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package NetPathMiner_1.40.0.tar.gz
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