KGML2igraph
(Package: NetPathMiner) :
Processes KGML files into igraph objects
This function takes KGML files as input, and returns either a metabolic or a signaling network as output.
● Data Source:
BioConductor
● Keywords:
● Alias: KGML2igraph
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These functions deals with conforming with MIRIAM annotation guidelines, conversion and mapping between MIRIAM identifiers.
● Data Source:
BioConductor
● Keywords:
● Alias: fetchAttribute, stdAttrNames
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This function gets a NetPathMiner default value for a variable.
● Data Source:
BioConductor
● Keywords:
● Alias: NPMdefaults
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NetPathMiner-package
(Package: NetPathMiner) :
General framework for network extraction, path mining.
NetPathMiner implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. NetPathMiner supports construction of various types of genome scale networks from KGML, SBML and BioPAX formats, enabling its utility to most common pathway databases. NetPathMiner also provides different visualization techniques to facilitate the analysis of even thousands of output paths.
● Data Source:
BioConductor
● Keywords:
● Alias: NPM, NetPathMiner, NetPathMiner-package
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SBML2igraph
(Package: NetPathMiner) :
Processes SBML files into igraph objects
This function takes SBML files as input, and returns either a metabolic or a signaling network as output.
● Data Source:
BioConductor
● Keywords:
● Alias: SBML2igraph
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This function computes edge weights based on a gene expression profile.
● Data Source:
BioConductor
● Keywords:
● Alias: assignEdgeWeights
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biopax2igraph
(Package: NetPathMiner) :
Processes BioPAX objects into igraph objects
This function takes BioPAX objects (level 2 or 3) as input, and returns either a metabolic or a signaling network as output.
● Data Source:
BioConductor
● Keywords:
● Alias: biopax2igraph
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colorVertexByAttr
(Package: NetPathMiner) :
Computes colors for vertices according to their attributes.
This function returns a list of colors for vertices, assigned similar colors if they share a common attribute (ex: in the same pathway, etc).
● Data Source:
BioConductor
● Keywords:
● Alias: colorVertexByAttr
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A dataset containing Porphyrin metabolism pathway in Biopax Level 3 and parsed with readBiopax.
● Data Source:
BioConductor
● Keywords:
● Alias: ex_biopax
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ex_kgml_sig
(Package: NetPathMiner) :
Singaling network from KGML example
An example igraph object representing Ras and chemokine signaling pathways in human extracted from KGML files.
● Data Source:
BioConductor
● Keywords:
● Alias: ex_kgml_sig
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providing 
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