rBiopaxParser statistics

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Citations per year

Number of citations per year for the bioinformatics software tool rBiopaxParser
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Tool usage distribution map

This map represents all the scientific publications referring to rBiopaxParser per scientific context
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Protocols

rBiopaxParser specifications

Information


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
Requirements
BiocGenerics, RUnit, data.table, R(>=3.0.0), graph, RBGL, RCurl, Rgraphviz, igraph, XML, nem
Maintained Yes

Versioning


No version available

Documentation


Publication for rBiopaxParser

rBiopaxParser citations

 (3)
library_books

Building pathway graphs from BioPAX data in R

2016
F1000Res
PMCID: 5130076
PMID: 27990265
DOI: 10.5256/f1000research.10320.r17096

[…] Software available from: The function pathway2Graph is available in the latest version of the R package rBiopaxParser and can be installed from Bioconductor. Latest source code: https://github.com/frankkramer-lab/rBiopaxParser/tree/2.12.0 Archived source code as at the time of publication: http://dx.do […]

library_books

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

2015
PLoS One
PMCID: 4669165
PMID: 26632845
DOI: 10.1371/journal.pone.0144014

[…] s of WNT networks originating from the public microarray expression data and the newly generated RNA-Seq data were investigated for graph overlaps. Therefore, the calcGraphOverlap R-function from the rBiopaxParser R-package was utilized and the modules based on microarray data were used as reference graphs. […]

call_split

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

2014
Biology
PMCID: 4009765
PMID: 24833336
DOI: 10.3390/biology3010085
call_split See protocol

[…] ilar to Cytoscape, especially focused on visualizing extremely large networks. CePa provides preset plotting parameters for its supplied igraph objects. The packages NCIgraph, KEGGgraph, pathview and rBiopaxParser enable the user to plot pathways via Rgraphviz. Package pathview additionally provides a function to export native KEGG representations as PNG image files. The graphite package, which us […]


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

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