To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")

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

paxtoolsr

 

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

Bioconductor version: Release (3.1)

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 is not available
source("https://bioconductor.org/biocLite.R")
biocLite("paxtoolsr")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("paxtoolsr")

 

HTML R Script Using PaxtoolsR
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneSetEnrichment, GraphAndNetwork, Network, NetworkEnrichment, Pathways, Software, SystemsBiology
Version 1.2.1
In Bioconductor since BioC 3.0 (R-3.1) (1 year)
License LGPL-3
Depends R (>= 3.1.1), rJava (>= 0.9-4), XML, RCurl, rjson, plyr
Imports
LinkingTo
Suggests testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, igraph, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma
SystemRequirements Java (>= 1.5)
Enhances
URL https://bitbucket.org/cbio_mskcc/paxtoolsr
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source paxtoolsr_1.2.1.tar.gz
Windows Binary paxtoolsr_1.2.1.zip
Mac OS X 10.6 (Snow Leopard) paxtoolsr_1.2.1.tgz
Mac OS X 10.9 (Mavericks) paxtoolsr_1.2.1.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/paxtoolsr/tree/release-3.1
Package Short Url http://bioconductor.org/packages/paxtoolsr/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center