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.

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>
Date of publicationNone
MaintainerAhmed Mohamed <mohamed@kuicr.kyoto-u.ac.jp>
LicenseGPL (>= 2)
Version1.10.0
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...

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

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