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rBiopaxParser specifications


Unique identifier OMICS_05211
Name rBiopaxParser
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.20.0
Stability Stable
BiocGenerics, RUnit, data.table, R(>=3.0.0), graph, RBGL, RCurl, Rgraphviz, igraph, XML, nem
Maintained Yes


No version available


Publication for rBiopaxParser

rBiopaxParser citations


Building pathway graphs from BioPAX data in R

PMCID: 5130076
PMID: 27990265
DOI: 10.5256/f1000research.10320.r17096

[…] pathways are increasingly available in the biopax format which uses an rdf model for data storage. one can retrieve the information in this data model in the scripting language r using the package rbiopaxparser, which converts the biopax format to one readable in r. it also has a function to build a regulatory network from the pathway information. here we describe an extension […]


Newly Constructed Network Models of Different WNT Signaling Cascades Applied to Breast Cancer Expression Data

PMCID: 4669165
PMID: 26632845
DOI: 10.1371/journal.pone.0144014

[…] of genes and genomes (kegg) [], pathway interaction database (pid) [] and pathway commons []. the database exports of biopax level 3 files were downloaded in march 2014 and parsed into r using the rbiopaxparser r-package []. pathways of interest were selected according to the presence of key words such as 'wnt', 'catenin', and 'pcp' either within pathway names or their members. the pathways […]


Comparative study on gene set and pathway topology based enrichment methods

PMCID: 4618947
PMID: 26489510
DOI: 10.1186/s12859-015-0751-5

[…] of the evaluated algorithms we supplied all methods with the same kegg pathway data., a biopax level 3 export of kegg pathway database was downloaded on march 2013 and parsed into r using the rbiopaxparser r-package [] (fig. ). non-metabolic pathways were selected and transformed into interaction graphs in which the nodes represent genes and the directed edges represent activation […]


Tools for visualization and analysis of molecular networks, pathways, and omics data

PMCID: 4461095
PMID: 26082651
DOI: 10.2147/AABC.S63534

[…] molecular interaction vocabularies, as well as its own community-defined constructs., several tools have been developed to read and process biopax files. these include libraries like paxtools, rbiopaxparser, and biopax-pattern, and visualization and analysis tools like cytoscape and cypath2, among others., however useful, the primary goal of biopax is not to satisfy data visualization […]


A global microRNA screen identifies regulators of the ErbB receptor signaling network

PMCID: 4314810
PMID: 25630670
DOI: 10.1186/s12964-015-0084-z

[…] (figure b).figure 3, for network construction we used data from the reactome database [] and identified 24 pathways connected to erbb/akt signaling. these pathways were parsed into r using r-package rbiopaxparser [] as directed graphs. next, 24 graphs were merged into a single signaling network, comprising 312 nodes representing genes, and 3582 edges representing activation or inhibition […]


R Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

PMCID: 4009765
PMID: 24833336
DOI: 10.3390/biology3010085

[…] package psicquic [] retrieves interactions and annotations in the psi mi format via web services offering psi mi query capabilities and returns these as lists of interactions within r. finally, the rbiopaxparser parses arbitrary biopax level 2 and level 3 databases using the xml package and represents them in r []., another criterion for pathway data integration is the extent of data […]

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rBiopaxParser institution(s)
Department of Medical Statistics, University Medical Center Göttingen, Germany

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