makeReactionNetwork

graph

An option to remove translocation and spontaneous reactions that require
no catalyzing genes. Translocation reactions are detected from reaction name (SBML, BioPAX), or
by having identical substrates and products.

simplify


This function removes metabolite nodes keeping them as edge attributes. The resulting
network contains reaction nodes only, where edges indicate that a metabolite produced
by one reaction is consumed by the other.


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.

Ahmed Mohamed

NetPathMiner

NetPathMiner for Biological Network Construction, Path Mining
and Visualization

makeReactionNetwork function

This function removes metabolite nodes keeping them as edge attributes. The resulting
network contains reaction nodes only, where edges indicate that a metabolite produced
by one reaction is consumed by the other.

makeReactionNetwork: Convert metabolic network to reaction network.

Description

Usage

Arguments

Value

See Also

Examples