Package: NetPathMiner 1.43.0

Ahmed Mohamed

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.

Authors:Ahmed Mohamed [aut, cre], Tim Hancock [aut], Tim Hancock [aut]

NetPathMiner_1.43.0.tar.gz

NetPathMiner_1.43.0.tgz(r-4.4-x86_64)NetPathMiner_1.43.0.tgz(r-4.4-arm64)NetPathMiner_1.43.0.tgz(r-4.3-x86_64)NetPathMiner_1.43.0.tgz(r-4.3-arm64)
NetPathMiner_1.43.0.tar.gz(r-4.5-noble)NetPathMiner_1.43.0.tar.gz(r-4.4-noble)
NetPathMiner.pdf |NetPathMiner.html✨
NetPathMiner/json (API)
NEWS

# Install 'NetPathMiner' in R:

install.packages('NetPathMiner', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ahmohamed/netpathminer/issues

Uses libs:

libsbml– System Biology Markup Language library
libxml2– GNOME XML library
openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

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

On BioConductor:NetPathMiner-1.41.3(bioc 3.20)NetPathMiner-1.40.2(bioc 3.19)

graphandnetwork pathways network clustering classification

6.45 score 7 stars 9 scripts 170 downloads 2 mentions 44 exports 11 dependencies

Last updated 23 days agofrom:271cd7acb2. Checks:OK: 1 NOTE: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-linux-x86_64	NOTE	Oct 30 2024
R-4.4-mac-x86_64	NOTE	Oct 30 2024
R-4.4-mac-aarch64	NOTE	Oct 30 2024
R-4.3-mac-x86_64	NOTE	Oct 30 2024
R-4.3-mac-aarch64	NOTE	Oct 30 2024

Exports:assignEdgeWeights biopax2igraph colorVertexByAttr expandComplexes extractPathNetwork fetchAttribute getAttribute getAttrNames getAttrStatus getGeneSetNetworks getGeneSets getPathsAsEIDs KGML2igraph layoutVertexByAttr makeGeneNetwork makeMetaboliteNetwork makeReactionNetwork NPMdefaults pathClassifier pathCluster pathRanker pathsToBinary plotAllNetworks plotClassifierROC plotClusterMatrix plotClusterProbs plotClusters plotCytoscapeGML plotNetwork plotPathClassifier plotPathCluster plotPaths predictPathClassifier predictPathCluster registerMemoryErr reindexNetwork rmAttribute rmSmallCompounds SBML2igraph setAttribute simplifyReactionNetwork stdAttrNames toGraphNEL vertexDeleteReconnect

Dependencies:cli cpp11 glue igraph lattice lifecycle magrittr Matrix pkgconfig rlang vctrs

Workflow for NetPathMiner

Ahmed Mohamed

Rendered fromNPMVignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-04-01
Started: 2019-03-02

Citation

Development and contributors

Readme and manuals

Help Manual

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