To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")

In most cases, you don't need to download the package archive at all.

paxtoolsr

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see paxtoolsr.

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

Bioconductor version: 3.4

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 cbio.mskcc.org>

Citation (from within R, enter citation("paxtoolsr")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")

Documentation

HTML R Script Using PaxtoolsR
PDF Reference Manual
Text NEWS

Details

biocViews GeneSetEnrichment, GraphAndNetwork, KEGG, Network, NetworkEnrichment, Pathways, Reactome, Software, SystemsBiology
Version 1.8.0
In Bioconductor since BioC 3.0 (R-3.1) (2.5 years)
License LGPL-3
Depends R (>= 3.2), rJava (>= 0.9-4), XML
Imports httr, igraph, plyr, rjson, R.utils, data.table
LinkingTo
Suggests testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW, parallel
SystemRequirements Java (>= 1.6)
Enhances
URL https://github.com/BioPAX/paxtoolsr
Depends On Me
Imports Me
Suggests Me RCy3
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source paxtoolsr_1.8.0.tar.gz
Windows Binary paxtoolsr_1.8.0.zip
Mac OS X 10.9 (Mavericks) paxtoolsr_1.8.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/paxtoolsr/tree/release-3.4
Package Short Url http://bioconductor.org/packages/paxtoolsr/
Package Downloads Report Download Stats

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