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PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

Bioconductor version: 3.0

The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC). Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.

Author: Augustin Luna

Maintainer: Augustin Luna <lunaa at>

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HTML R Script Using PaxtoolsR
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Text   NEWS


biocViews GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, SystemsBiology
Version 1.2.11
In Bioconductor since BioC 3.0 (R-3.1)
License LGPL-3
Depends R (>= 3.1.1), rJava (>= 0.9-4), XML, RCurl, rjson, plyr
Suggests testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, igraph, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma
SystemRequirements Java (>= 1.5)
Depends On Me
Imports Me
Suggests Me
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