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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("NetPathMiner")
AuthorAhmed 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>
Bioconductor views Classification Clustering GraphAndNetwork Network Pathways
Date of publicationNone
MaintainerAhmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>
LicenseGPL (>= 2)
Version1.12.0
https://github.com/ahmohamed/NetPathMiner

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...

Functions

assignEdgeWeights Man page
biopax2igraph Man page
colorVertexByAttr Man page
ex_biopax Man page
ex_kgml_sig Man page
ex_microarray Man page
expandComplexes Man page
ex_sbml Man page
extractPathNetwork Man page
fetchAttribute Man page
getAttribute Man page
getAttrNames Man page
getAttrStatus Man page
getGeneSetNetworks Man page
getGeneSets Man page
getPathsAsEIDs Man page
KGML2igraph Man page
layoutVertexByAttr Man page
makeGeneNetwork Man page
makeReactionNetwork Man page
NetPathMiner Man page
NetPathMiner-package Man page
NPM Man page
NPMdefaults Man page
pathClassifier Man page
pathCluster Man page
pathRanker Man page
pathsToBinary Man page
plotAllNetworks Man page
plotClassifierROC Man page
plotClusterMatrix Man page
plotClusterProbs Man page
plotClusters Man page
plotCytoscapeGML Man page
plotNetwork Man page
plotPathClassifier Man page
plotPathCluster Man page
plotPaths Man page
predictPathClassifier Man page
predictPathCluster Man page
registerMemoryErr Man page
rmAttribute Man page
rmSmallCompounds Man page
samplePaths Man page
SBML2igraph Man page
setAttribute Man page
simplifyReactionNetwork Man page
stdAttrNames Man page
toGraphNEL Man page
vertexDeleteReconnect Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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