rBiopaxParser statistics

You need an account to access this content


Citations per year

Citations chart

Popular tool citations

chevron_left Network visualization chevron_right
Popular tools chart

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

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


Add your version


Publication for rBiopaxParser

rBiopaxParser in publications

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 […]

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 […]

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 […]

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 […]

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 […]

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

rBiopaxParser reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review rBiopaxParser