NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

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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 <mohamed@kuicr.kyoto-u.ac.jp>, Tim Hancock <timothy.hancock@kuicr.kyoto-u.ac.jp>, Ichigaku Takigawa <takigawa@kuicr.kyoto-u.ac.jp>, Nicolas Wicker <nicolas.wicker@unistra.fr>
Date of publication
None
Maintainer
Ahmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>
License
GPL (>= 2)
Version
1.10.0
URLs

View on Bioconductor

Man pages

assignEdgeWeights
Assigning weights to network edges
biopax2igraph
Processes BioPAX objects into igraph objects
colorVertexByAttr
Computes colors for vertices according to their attributes.
ex_biopax
Biopax example data
ex_kgml_sig
Singaling network from KGML example
ex_microarray
An microarray data example.
ex_sbml
Metabolic network from SBML example
extractPathNetwork
Creates a subnetwork from a ranked path list
getAttr
Get / Set vertex attribute names and coverage
getGeneSetNetworks
Generate geneset networks from an annotated network.
getGeneSets
Generate genesets from an annotated network.
getPathsAsEIDs
Convert a ranked path list to edge ids of a graph
KGML2igraph
Processes KGML files into igraph objects
layoutVertexByAttr
A graph layout function, which groups vertices by attribute.
makeGeneNetwork
Expand reactions / complexes into their gene constituents.
makeReactionNetwork
Convert metabolic network to reaction network.
MIRIAM
MIRIAM annotation attributes
NetPathMiner-package
General framework for network extraction, path mining.
NPMdefaults
Default values for NetPathMiner
pathClassifier
HME3M Markov pathway classifier.
pathCluster
3M Markov mixture model for clustering pathways
pathRanker
Extracting and ranking paths from a network
pathsToBinary
Converts the result from pathRanker into something suitable...
plotAllNetworks
Higlighting ranked paths over multiple network...
plotClassifierROC
Diagnostic plots for pathClassifier.
plotClusters
Plots the structure of all path clusters
plotCytoscape
Plots an annotated igraph object in Cytoscape.
plotNetwork
Plots an annotated igraph object.
plotPathClassifier
Plots the structure of specified path found by...
plotPathCluster
Plots the structure of specified path cluster
plotPaths
Plots an annotated igraph object higlighting ranked paths.
predictPathClassifier
Predicts new paths given a pathClassifier model.
predictPathCluster
Predicts new paths given a pathCluster model
registerMemoryErr
Internal method to register memery errors.
rmSmallCompounds
Remove uniquitous compounds from a metabolic network
samplePaths
Creates a set of sample path p-values for each length given a...
SBML2igraph
Processes SBML files into igraph objects
simplifyReactionNetwork
Removes reactions with no gene annotations
toGraphNEL
Converts an annotated igraph object to graphNEL
vertexDeleteReconnect
Network editing: removing vertices and connecting their...

Files in this package

NetPathMiner/.BBSoptions
NetPathMiner/DESCRIPTION
NetPathMiner/NAMESPACE
NetPathMiner/NEWS
NetPathMiner/R
NetPathMiner/R/NPM-package.R
NetPathMiner/R/dbExtract.R
NetPathMiner/R/netProcess.R
NetPathMiner/R/netWeight.R
NetPathMiner/R/pathClassifier.R
NetPathMiner/R/pathCluster.R
NetPathMiner/R/pathRank.R
NetPathMiner/R/plotPath.R
NetPathMiner/README.md
NetPathMiner/build
NetPathMiner/build/vignette.rds
NetPathMiner/cleanup
NetPathMiner/cleanup.win
NetPathMiner/configure
NetPathMiner/configure.ac
NetPathMiner/configure.win
NetPathMiner/data
NetPathMiner/data/ex_biopax.rda
NetPathMiner/data/ex_kgml_sig.rda
NetPathMiner/data/ex_microarray.rda
NetPathMiner/data/ex_sbml.rda
NetPathMiner/inst
NetPathMiner/inst/CITATION
NetPathMiner/inst/doc
NetPathMiner/inst/doc/NPMVignette.R
NetPathMiner/inst/doc/NPMVignette.Rnw
NetPathMiner/inst/doc/NPMVignette.pdf
NetPathMiner/inst/extdata
NetPathMiner/inst/extdata/env_data.RData
NetPathMiner/inst/extdata/hsa00860.xml
NetPathMiner/inst/extdata/porphyrin.sbml
NetPathMiner/man
NetPathMiner/man/KGML2igraph.Rd
NetPathMiner/man/MIRIAM.Rd
NetPathMiner/man/NPMdefaults.Rd
NetPathMiner/man/NetPathMiner-package.Rd
NetPathMiner/man/SBML2igraph.Rd
NetPathMiner/man/assignEdgeWeights.Rd
NetPathMiner/man/biopax2igraph.Rd
NetPathMiner/man/colorVertexByAttr.Rd
NetPathMiner/man/ex_biopax.Rd
NetPathMiner/man/ex_kgml_sig.Rd
NetPathMiner/man/ex_microarray.Rd
NetPathMiner/man/ex_sbml.Rd
NetPathMiner/man/extractPathNetwork.Rd
NetPathMiner/man/getAttr.Rd
NetPathMiner/man/getGeneSetNetworks.Rd
NetPathMiner/man/getGeneSets.Rd
NetPathMiner/man/getPathsAsEIDs.Rd
NetPathMiner/man/layoutVertexByAttr.Rd
NetPathMiner/man/makeGeneNetwork.Rd
NetPathMiner/man/makeReactionNetwork.Rd
NetPathMiner/man/pathClassifier.Rd
NetPathMiner/man/pathCluster.Rd
NetPathMiner/man/pathRanker.Rd
NetPathMiner/man/pathsToBinary.Rd
NetPathMiner/man/plotAllNetworks.Rd
NetPathMiner/man/plotClassifierROC.Rd
NetPathMiner/man/plotClusters.Rd
NetPathMiner/man/plotCytoscape.Rd
NetPathMiner/man/plotNetwork.Rd
NetPathMiner/man/plotPathClassifier.Rd
NetPathMiner/man/plotPathCluster.Rd
NetPathMiner/man/plotPaths.Rd
NetPathMiner/man/predictPathClassifier.Rd
NetPathMiner/man/predictPathCluster.Rd
NetPathMiner/man/registerMemoryErr.Rd
NetPathMiner/man/rmSmallCompounds.Rd
NetPathMiner/man/samplePaths.Rd
NetPathMiner/man/simplifyReactionNetwork.Rd
NetPathMiner/man/toGraphNEL.Rd
NetPathMiner/man/vertexDeleteReconnect.Rd
NetPathMiner/src
NetPathMiner/src/Makevars.in
NetPathMiner/src/PathRanker.cpp
NetPathMiner/src/boost.tar.gz
NetPathMiner/src/handlesegfault.c
NetPathMiner/src/handlesegfault.h
NetPathMiner/src/hme3m.c
NetPathMiner/src/hme3m.h
NetPathMiner/src/init.c
NetPathMiner/src/init.h
NetPathMiner/src/kgml_interface.cpp
NetPathMiner/src/methods.cpp
NetPathMiner/src/pathScope.cpp
NetPathMiner/src/sbml_interface.cpp
NetPathMiner/src/sbml_interface.h
NetPathMiner/vignettes
NetPathMiner/vignettes/NPMVignette.Rnw
NetPathMiner/vignettes/ROCplot.pdf
NetPathMiner/vignettes/example.R